Abstract Marine fish trypanosomes are widespread hemoparasites that pose significant threats to wild and farmed teleosts, yet they remain genomically underrepresented compared to their mammalian-infecting counterparts. Here, we present the first chromosome-level, gap-free genome assembly of Trypanosoma larimichthysi , a recently described species causing severe trypanosomiasis outbreaks in the economically important large yellow croaker ( Larimichthys crocea ) along the Chinese coast. The assembly, generated using PacBio HiFi long-read sequencing combined with Hi-C chromatin conformation capture, spans 51.04 Mb across exactly 35 pseudochromosomes, with a contig N50 of 1.43 Mb and 97.96% of sequences anchored. Exceptional completeness is evidenced by telomere-to-telomere resolution for 25 chromosomes (58 telomeric loci captured in total), a 99.99% HiFi read mapping rate, and > 99% BUSCO completeness. The genome encodes 10,172 protein-coding genes, with repetitive sequences comprising 50.33%, dominated by retrotransposons including LINE and LTR elements. Comparative genomic analyses confirm the phylogenetic placement of T. larimichthysi within Trypanosoma and reveal lineage-specific gene family expansions potentially linked to host adaptation and pathogenicity. This reference-grade genome fills a critical gap in aquatic trypanosomatid genomics and provides a valuable resource for investigating parasite evolution, host–parasite interactions, antigenic variation mechanisms, and disease management strategies in mariculture.
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