Lindaspio polybranchiata is a deep-sea spionid annelid and an early colonizer of cold seep ecosystems, but genomic resources for this genus remain limited. Here, we present haplotype-resolved chromosome-level genome assemblies for L. polybranchiata generated using PacBio HiFi, Illumina, Hi-C, and RNA-seq data. The phased assembly comprises two haplotypes, A and B, with genome sizes of 1.72 Gb and 1.38 Gb, scaffold N50 values of 76.1 Mb and 71.0 Mb, and 81.5% and 92.8% of sequences anchored to 18 pseudochromosomes, respectively. BUSCO completeness reached 91.2% for haplotype A and 91.7% for haplotype B. We predicted 22,322 protein-coding genes in haplotype A and 19,587 in haplotype B, of which 88.80% and 85.21% were functionally annotated, respectively. These genome resources provide a foundation for studies of chromosome organization, comparative genomics, deep-sea adaptation, and the evolution of Lindaspio and related spionid annelids.
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