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.

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.

To describe the species composition of fish larvae and juveniles in the Nanji Islands, monthly collection was conducted at 12 stations around the Nanji Islands from March 2023 to February 2024 by using horizontal tow at the surface layer. The fish larvae and juveniles were collected by a larva net (1.3 m mouth diameter, 0.5 mm mesh aperture). A total of 6446 fish larvae and juveniles were collected, belonging to 59 species and 54 genera in 11 families. Most of them were preflexion larvae (93.31%). Gobiidae, with eight species, was the most diverse family. Based on the index of relative importance (IRI) result, the dominant species was Sebastiscus marmoratus (Cuvier, 1829), accounting for 84.52% of the total number of samples collected. The common species were Stolephorus commersonii Lacepède, 1803; Omobranchus elegans (Steindachner, 1876); Nibea albiflora (Richardson, 1846); Parablennius yatabei (Jordan & Snyder, 1900); Lateolabrax maculatus (McClelland, 1844); and Odontamblyopus lacepediiand (Temminck & Schlegel, 1845). Other species were all rare species. The highest species number was in September (18 species), and the highest density was in December. Only one fish larva was collected in April. Pielou’s evenness index was highest in November, while Margalef’s richness index and Shannon–Wiener diversity were highest in September. The result of cluster analysis showed that the 11 months (except April) could be divided into four groups. The species number, density, and three diversity indexes showed no significant correlation with temperature and salinity.

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.