The systematic status of the genus Cyclocheilichthys remains ambiguous due to a lack of comprehensive morphological and molecular evidence. Hence, this study represents the novel mitogenome of Cyclocheilichthys repasson to characterize its architecture and clarify its phylogenetic placement within the clade “Poropuntiinae.” The circular mitogenome was 16,571 base pairs in length and comprised 37 genes and a control region (CR). Most genes were encoded on the heavy strand, with the exception of ND6 and eight tRNA genes located on the light strand. The genome exhibited an A + T bias of approximately 57.7% and displayed distinct AT‐ and GC‐skew patterns. All protein‐coding genes (PCGs) initiated with the standard ATG start codon, except for COI , which began with GTG. The amino acid composition was dominated by leucine, serine, threonine, and isoleucine, and the ratio of nonsynonymous to synonymous substitutions suggested strong purifying selection across all PCGs. The majority of transfer RNA genes exhibited the canonical cloverleaf secondary structure, with the exception of tRNA‐Ser, which lacked the dihydrouridine (D) stem. The comparative analysis of 24 “Poropuntiinae” species revealed four conserved sequence blocks within the CR, while tandem repeat motifs were exclusively detected in 11 species and absent in C. repasson . The mitogenome‐based phylogenetic analyses using Bayesian and Maximum Likelihood methods supported the monophyly of Cyclocheilichthys and sister relationship of C. repasson with C. janthochir and C. apogon . The partial COI‐based investigation further revealed potential cryptic diversity within C. repasson populations from both mainland (Laos) and island (Sumatra, Indonesia), as indicated by a genetic divergence of 1.06%. This population separation may have been influenced by historical paleo‐river networks across Southeast Asia/Sunda Shelf during periods of lower sea levels. Collectively, these findings offer valuable insights into the structural features of the mitochondrial genome and elucidate the evolutionary history among cyprinid fishes.

The Bagridae (Actinopteri: Siluriformes) catfish Hemibagrus velox, endemic to Sumatra, Indonesia, raises critical taxonomic concerns due to limited molecul

The family Notopteridae is distributed across Africa and Asia and plays an important role in ecological functioning, local economies, and conservation initiatives. However, mitogenomic data for notopterids from the Sundaland hotspot remain scarce, limiting comprehensive understanding of their genetic architecture and matrilineal evolutionary history. To address this knowledge gap, the present study reports the first complete mitochondrial genome of Chitala borneensis and re‐sequences the mitogenome of Chitala lopis , two sympatric species endemic to Sundaland. Both Chitala mitogenomes exhibit the canonical teleost mitochondrial organization, comprising 37 genes and an AT‐rich control region, with C. borneensis (16,943 bp) representing the longest mitogenome reported within the genus to date. The codon usage analyses revealed a bias toward arginine, leucine, and serine, while nonsynonymous‐to‐synonymous substitution rate estimates indicated that most protein‐coding genes are evolving under purifying selection. The phylogenetic analyses recovered well‐supported African and Asian notopterid clades, with C. borneensis resolved as the sister lineage to C. lopis . Nevertheless, mitogenomic‐ and COI‐based phylogenetic frameworks inferred using Bayesian inference and maximum‐likelihood approaches supported multiple hypotheses regarding the systematic positions of mainland and island Chitala species in Southeast Asia. The divergence time estimates were congruent with historical biogeographic reconstructions, suggesting that Miocene tectonic events played a major role in the diversification of Chitala from other Asian notopterids. Furthermore, paleodrainage reorganization during the Last Glacial Maximum appears to have been critical in shaping the contemporary population structure of Chitala across the insular landscapes of this region. Collectively, this study provides new insights into the matrilineal evolutionary history of African and Asian notopterids, with particular emphasis on Sundaic Chitala species. The findings underscore the need for expanded taxon sampling and additional molecular data to improve population monitoring, inform conservation genetics, and ensure the long‐term persistence of these freshwater fishes within this biodiversity hotspot.

Butidae is a family of teleost fishes with diverse morphological and ecological adaptations, including the marbled goby (Oxyeleotris marmorata), a large species of high economic value in Southeast and East Asia. The previous mitogenomic studies on cultured populations of O. marmorata from non-native habitats have provided limited insights into genetic divergence, structural variation, and evolutionary relationships. Hence, this study presented the complete mitochondrial genome of O. marmorata from its native habitat in Indonesia, providing structural characterization, assessment of genetic diversity, and matrilineal phylogenetic analysis. The circular mitogenome was 16,525 bp, comprising 37 genes and a non-coding control region (CR). The gene organization and strand distribution were conserved among Oxyeleotris species, with 28 genes on the heavy strand and nine on the light strand, and a pronounced A+T compositional bias. The comparative analyses of O. marmorata (from both native and cultured habitats) and Oxyeleotris lineolata mitogenomes revealed minor variations in intergenic spacers, gene overlaps, protein-coding gene (PCGs) lengths, and codon usage patterns. Conversely, the nonsynonymous and synonymous substitution ratios observed in species of the family Butidae and its closest related family (Eleotridae) indicate strong purifying selection in the present dataset. Notably, the ATG was the predominant start codon, whereas the COI gene utilized GTG, and amino acid composition analysis demonstrated high frequencies of arginine, leucine, and serine. Most transfer RNAs retained the canonical cloverleaf secondary structure except for trnS1, which lacked a functional dihydrouridine arm, whereas the CR contained four conserved sequence blocks with variable nucleotide motifs and no detectable tandem repeats. The haplotype analysis of native (Indonesia) and introduced populations (China) highlighted three haplotypes with high diversity (Hd = 1.0000) and substantial nucleotide variation (π = 0.6667). The genetic divergence across 13 PCGs was gene-specific, with COI and ND5 showing the highest variation, while ND4L and ATP8 were highly conserved. The phylogenetic analyses based on concatenated 13 PCGs using both Bayesian Inference and Maximum Likelihood methods revealed that Oxyeleotris forms a monophyletic clade and is closely related to Bostrychus sinensis. In addition, the broader phylogenetic framework inferred the matrilineal relationships within the family Butidae and its closest related family, Eleotridae. This study also recommends expanding analyses to include the mitogenomes of the remaining 17 Oxyeleotris species, together with comprehensive genomic data, to further elucidate their genetic architecture, evolutionary history, and ecological adaptability across diverse aquatic ecosystems.

Despite its ecological and economic importance, Hampala macrolepidota (Cyprinidae: Smiliogastrinae) remains taxonomically debated, having undergone historical reclassifications across multiple taxonomic ranks. These challenges highlight the urgent need for integrative genomic analyses to resolve its phylogeny and assess genome-wide diversity, establishing a baseline for effective management and conservation. In this study, the newly assembled mitogenome of H. macrolepidota from within its native range in Lake Dibawah, West Sumatra, Indonesia, was sequenced. The mitogenome spanned 17,104 bp, encoded 37 genes and a control region, and exhibited a nucleotide composition biased toward adenine and thymine. The protein-coding genes (PCGs) predominantly utilized ATG as the initiation codon and showed a higher proportion of hydrophobic compared to hydrophilic amino acids. The nonsynonymous (Ka) and synonymous (Ks) substitution ratios were below ‘1’, which indicates negative selection on most of the PCGs within Hampala and other Smiliogastrinae species. Mitogenome-wide analysis revealed overall high intraspecific genetic diversity (≥2.7%) in the native Indonesian population compared to mainland populations in Southeast Asia. The Bayesian and maximum-likelihood phylogenetic analyses elucidated matrilineal evolutionary relationships within the subfamily Smiliogastrinae, with the Hampala species forming a monophyletic cluster. The present mitogenome-based phylogenetic topologies also supported the taxonomic placement of several species in the revised classification, which previously were classified under the genera Puntius and Barbus, respectively. Additionally, the investigation of partial mitochondrial COI and Cytb genes further elucidated the population genetic structure of H. macrolepidota across Southeast and East Asia. The observed genetic divergence (0–4.2% in COI and 0–4.5% in Cytb), together with well-resolved phylogenetic clustering and the presence of both shared and distinct haplotypes among Indonesian samples, provides strong evidence for long-term population isolation and local adaptation. These patterns are most plausibly driven by historical hydrological dynamics, paleo-drainage connectivity, and persistent geographic barriers that have structured population divergence over time. In addition, this study emphasizes the need to generate mitogenomes of seven additional Hampala species from Southeast Asia to better understand their evolutionary patterns. Further, broader sampling of wild H. macrolepidota populations across their biogeographical range will be essential to strengthen understanding of their genetic diversity and guide effective conservation strategies.