This study employed environmental DNA (eDNA) technology to investigate the diversity of plankton, benthic invertebrates, and fish in the Jingjiang section of the Yangtze River. A total of 216 water samples were collected from three sites across four seasons during 2023–2024. Alpha diversity indices (Shannon, Simpson, Chao1, and Pielou_J) and beta diversity analysis (NMDS) revealed that seasonal variation significantly influenced community composition, whereas spatial differences were not significant (PERMANOVA, p > 0.05), likely due to strong hydrodynamics and highwater connectivity. Plankton were the most sensitive to seasonal changes, fol-lowed by benthic invertebrates, while fish exhibited relatively weaker responses. Correlation analysis further demonstrated a clear positive relationship between Yangtze finless porpoise activity and aquatic biodiversity, with evidence of selective associations in habitat community composition. These findings indicate that com-munity characteristics may serve as ecological indicators of biodiversity within porpoise habitats. Overall, this study confirms the feasibility of eDNA technology for large-scale aquatic ecosystem monitoring and provides valuable data and meth-odological references for the conservation of the Yangtze finless porpoise and the assessment of aquatic ecological health.

Due to their maternal uniparental inheritance, structural conservation, and heterogeneous substitution rates, mitochondrial genomes are critical molecular markers for elucidating lineage diversification and reconstructing high-resolution phylogenetic trees in marine invertebrates. Before this study, only one complete mitochondrial genome was available for the family Calappidae. We present the first complete mitochondrial genome sequences for five Calappa crab species. These mitogenomes exhibit characteristic features including 37 genes, a high AT nucleotide bias, and structural variation such as incomplete stop codons in certain taxa. Phylogenomic analyses confirmed the monophyly of Calappidae. Positive selection analysis identified significant adaptive signals in the ATP6, ND2, and ND5 genes, indicating their critical roles in energy metabolism. All examined species of the superfamily Calappoidea conform to the ancestral gene order of Brachyura, with no rearrangement events detected. This conserved gene arrangement can serve as a reliable phylogenetic marker, although the molecular mechanisms underlying this stability require further investigation across additional brachyuran taxa. This study provides essential molecular resources for Calappidae systematics and Brachyuran evolutionary history, while underscoring the need to integrate future nuclear genomic data to refine higher- level phylogenies.