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.

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.