The complete mitochondrial genome and phylogenetic analysis for Leiognathus equula from the South China Sea was performed using shallow genome skimming. For accurate species identification and redescription, morphometric and meristic characters were examined and compared with previous descriptions. To facilitate the identification of species and to enable comparison with the mitochondrial genome phylogeny, molecular comparisons were conducted using three mitochondrial genes: large ribosomal RNA (16S rRNA), cytochrome c oxidase subunit 1 (COX1), and NADH dehydrogenase (ND5). The mitogenome (16 398 bp) comprised 38 mitochondrial genes, similar to most bony fishes: 13 protein-coding genes (PCGs), 2 rRNA and 22 transfer RNA genes, and 1 non-coding region. The complete mitogenome comprised 30.7% A, 24.2% T, 15.0% G, and 30.1% C. The A+T content (54.9%) was higher than the G+C content (45.1%). All PCGs started with the typical ATG codon, except COX1, which started with GTG. Seven PCGs ended with incomplete stop codons (TA or T). The Ka/Ks ratios of all PCGs were < 1, indicating purifying selection. The phylogenies of Leiognathidae, both based on the amino acid sequences of the 13 PCGs and the single genes 16S RNA and COX1, were monophyletic with high nodal support (> 75%). L. brevirostris (NC 026232) is believed to be a Nuchequula species, whereas L. ruconius (NC 057225) is not classified under Leiognathus in the NCBI database. The phylogenetic trees divided the Leiognathidae family into three clades. The mitogenome phylogeny suggested that the Leiognathidae and Chaetodontidae clades are sister groups. These findings provide important genetic data for population genetics research and a phylogenetic analysis of Leiognathidae.

The ponyfish genus Aurigequula is a relatively poorly studied group within the Leiognathidae, with its diversity and phylogenetic relationships in the West Pacific remaining unclear. This study reports the first confirmed record of Aurigequula striata from Chinese waters, based on two specimens obtained from a fish market in Sanya, Hainan Island. Newly collected specimens of A. fasciata from the same region are also provided, which enabled detailed morphological and genomic analysis. The morphological descriptions are supplemented by detailed photographic documentation of fresh and preserved specimens, addressing the historical scarcity of reliable visual references for these species. Furthermore, we present the first complete mitochondrial genomes for both A. striata (16,629 bp) and A. fasciata (16,537 bp). Our phylogenomic analysis, based on 13 protein-coding genes, strongly supports the monophyly of the subfamilies Gazzinae and Leiognathinae. Within Leiognathinae, however, the analysis suggests paraphyly of Aurigequula , with A. fasciata forming a clade with Leiognathus equula to the exclusion of A. striata . This result conflicts with the current morphology-based generic diagnosis, which relies on consistent differences in the length of the second dorsal-fin spine and body coloration patterns. This study significantly expands the genomic resources for the understudied genus Aurigequula but also highlights the limitations of relying solely on mitochondrial data for resolving generic-level relationships. A more robust phylogenetic framework for Leiognathidae, capable of reconciling molecular and morphological evidence, will require the integration of multiple independent nuclear loci.

During bottom trawl surveys carried out between 2013–2021, 52 specimens (33.8–54.0 mm SL) of Egglestone’s bumblebee goby Egglestonichthys bombylios were collected at a depth of 1.5–15 m from Dongshan Bay, Sanmen Bay, and Niushan Island, China. They represent the first records of this species from China. A full description, including fresh colouration of the species is provided as it is poorly known. The individuals collected in China agree with most morphological features of the holotype, except for the pelvic fin fraenum that was not observed or appears to be absent in most specimens. A strong relationship between E. bombylios, Larsonella pumilus, and the genus Priolepis is herein demonstrated by the mitochondrial genome sequences of E. bombylios and twenty closely related species. This study enriches the existing genetic data of the so-called Priolepis lineage and provides useful insights into the phylogenetic relationships across species of the genera Egglestonichthys, Priolepis, and Larsonella.

The ponyfish genus Nuchequula is presents taxonomic challenges within Leiognathidae due to morphological complexities and a lack of genomic resources. However, the absence of a complete mitochondrial genome for Nuchequula longicornis has hindered comprehensive phylogenetic comparisons. Here, we employed an integrative approach combining detailed morphology with molecular validation via 16S rRNA gene sequencing to confirm the identity of specimens from the Beibu Gulf. Furthermore, we present the first complete mitogenome of N. longicornis. This circular 16,514 bp molecule exhibits a typical gene order, a moderate AT bias (54.8%), and strong purifying selection across all protein-coding genes. Phylogenomic analysis based on the complete mitogenome reliably resolved the position of N. longicornis within Leiognathidae, contributing to the discussion on the phylogenetic relationships and potential monophyly of Nuchequula and contributing to the understanding of intra-familial relationships. Our study provides an essential mitogenomic resource for N. longicornis and offers insights into mitochondrial evolutionary patterns within this family.

This study documents the northernmost record of Egglestonichthys melanoptera in the South China Sea (Hainan Island, China), thereby extending its distribution in the Indo-Pacific region from the Indian Ocean, and confirms the sympatric occurrence of E. bombylios. The morphological characteristics of E. melanoptera are described in detail, and measurable data is presented. The complete mitochondrial genomes of both species have been presented for the first time (17,743 bp for E. bombylios, 17,350 bp for E. melanoptera), revealing a conserved gobiid genomic architecture with a pronounced A+T bias (60.3–62.7%) and codon position-specific nucleotide preferences. A further objective of this study was to construct a phylogeny of 110 species of the family Gobiidae, extending previous studies. Phylogenetic analyses resolved E. melanoptera within Gobiidae, supported by osteological synapomorphies (single epural; pterygo-phore formula 3-22110), and placed Egglestonichthys within the Priolepis lineage. The validity of Benthophilinae remains contentious due to conflicting swim bladder and spine morphology, necessitating integrative reassessment. Comparative mitogenomic analyses reveal that the mitochondrial genome currently attributed to Oxyurichthys formosanus in GenBank (accession: KC237282) does not represent the genus Oxyurichthys but should be reassigned to Cryptocentrus yatsui. A revised diagnostic key has been synthesised, synthesising historical descriptions with novel morphological-molecular data, giving taxonomy for Egglestonichthys species. These findings contribute to our understanding of the evolutionary trajectories of gobiid fish, emphasising the synergy of mitogenomic and morphological approaches in resolving complex marine fish systematics.

Neobythites nanhaiensis sp. nov ., a new cusk eel species from the South China Sea, is described based on 14 specimens collected at a depth of 400 m near Nan’an Reef. This species is readily distinguished from all congeners by the unique presence of two (rarely three) distinct black ocelli on the mid-flank, a trait absent in all other Neobythites species. It further lacks stripes, fin ocelli, or dark fin margins. The meristic features include dorsal-fin rays 107 (90–115), anal-fin rays 93 (80–94), pectoral-fin rays 25 (21–27), total vertebrae 62 (58–64), and 9–11 developed gill rakers. The complete mitochondrial genome (17,287 bp) was sequenced, exhibiting the typical vertebrate structure with an A+T bias of 55.1%. Phylogenetic analyses based on both the COI gene and the complete mitogenome robustly supported N. nanhaiensis sp. nov . as a distinct monophyletic lineage, sister to N. marginatus in the mitogenome phylogeny. This integrative taxonomic approach, combining morphology, meristics, otolith morphology, and mitogenomic data, confirms the establishment of this new species, which lies outside any existing species group within the genus due to its unique flank ocelli.