Iguanodectes geisleri and I. adujai are freshwater fish from South America. Their taxonomic status and phylogenetic relationships are uncertain due to limited molecular data. High-throughput sequencing was applied to obtain and annotate for the first time the complete mitochondrial genomes of I. geisleri and I. adujai to clarify their phylogenetic positions. Mitochondrial genome sequences of 73 Characoidei species were retrieved from GenBank, with Gyrinocheilus aymonieri and Microphysogobio alticorpus designated as outgroups. Phylogenetic trees were constructed using a mitochondrial protein-coding gene dataset and Maximum Likelihood and Bayesian Inference methods. The complete mitochondrial genome measured 16,774 and 16,802 bp, respectively. Both genomes exhibited highly conserved structures. Despite morphological similarities and a close phylogenetic relationship, differences were detected in genomic structure, base composition, codon usage bias, and the control region between the two species. The two species comprise a strongly supported monophyletic clade and are sister species but represent distinct, independent branches. I. geisleri and I. adujai have been recognized as distinct species based on morphological differences, and this study provides molecular confirmation of their separate taxonomic status. The study provides molecular data for the taxonomic identification of fishes of the genus, Iguanodectes, and foundational mitochondrial genomic data for Characiformes. The study advances research on the genetic evolution of this group and resource conservation.

Despite the endangered status of the Oriental Stork (Ciconia boyciana) on the IUCN Red List, a critical lack of contemporary mitochondrial genomic data from its core distribution areas in mainland China has hindered our understanding of the species’ long-term evolutionary stability and spatiotemporal variation. This study addresses this gap by sequencing and assembling the complete mitogenome (17,608 bp) of a contemporary individual from Hongze Lake, Jiangsu (PX682155), and conducting a rigorous comparative analysis against a historical reference sequence published 25 years ago in Japan (NC_002196). Our results demonstrate striking structural and functional conservation across a quarter-century span; the 13 protein-coding genes exhibit highly synchronized gene arrangements, base composition biases, and Relative Synonymous Codon Usage (RSCU) patterns, indicative of stringent purifying selection maintaining oxidative phosphorylation efficiency. While phylogenetic analysis reinforces its sister-group relationship with the White Stork (C. ciconia), significant length polymorphisms were identified within the D-loop control region, primarily driven by microsatellite repeat variations. These findings provide a vital genomic benchmark for mainland populations, offering high-resolution molecular markers essential for future large-scale assessments of geographic isolation and the refinement of targeted conservation strategies for this flagship wetland species.

The Neotropical cichlid genus Apistogramma represents one of the most taxonomically diverse and ecologically significant groups of South American freshwater fishes, yet its evolutionary history and species boundaries remain poorly understood due to a lack of comprehensive genomic resources. To address this gap, this study investigated the complete mitogenomic characteristics of six representative Apistogramma species (A. agassizii, A. allpahuayo, A. baenschi, A. nijsseni, A. resticulosa, and A. cacatuoides) to establish a robust molecular framework for species identification and phylogenetic reconstruction. The results showed that Apistogramma mitogenomes are highly conserved. All six Apistogramma species exhibited significant AT bias. Selection pressure analysis revealed that the Ka/Ks ratios for all 13 protein-coding genes were between 0 and 1, indicating that these genes were under purifying selection. Differential site analysis identified nad5, cox1, and nad4 as ideal molecular markers for rapid Apistogramma species identification owing to higher proportions of variable sites. Phylogenetic analysis recovered Apistogramma as a strongly supported monophyletic clade (BP = 100, PP = 1.00), within which A. nijsseni clustered with A. baenschi and A. cacatuoides with A. agassizii. These internal phylogenetic relationships are consistent with the calculated genetic distances and previous morphological groupings. These findings provide an important theoretical basis and data support for rapid species identification, genetic evolutionary research, and divergence time estimation within Apistogramma.