It is relatively poorly understood how vertebrates can survive and thrive in deep-sea environments (depths below 3,400 m that are characterized by high hydrostatic pressures, low temperatures, and sparse food resources). Here we report two high-quality chromosome-level genomes for deep-sea eels (Ilyophis sp1 and Ilyophis sp2). Combining Illumina reads, PacBio, and Hi-C technologies, we sequenced and assembled its genomes. The genome assemblies were 1494.88 Mb and 1469.15 Mb for Ilyophis sp1 and Ilyophis sp2, with scaffold N50 values of 121.13 Mb and 115.31 Mb, and genome annotation predicted 22,465 and 21,632 protein-coding genes respectively. Phylogenetic analyses indicated that these two deep-sea eels diverged from European eels ~111.9 million years ago (Mya) and likely evolved into two separate groups ~3.59 Mya. Comparative genomic analyses reveal that: (1) the positively selected cytoskeleton gene TUBGCP3 and the expanded family MLC1 may improve the cytoskeleton stability under high pressure; (2) the changes in protein sequences of Acox1 may enhance cell membrane fluidity and maintain transport activity under high pressure; (3) functional mutation of the translation gene HARS in deep-sea eels may change its translation ability to resist the influence of low temperature on translation-related enzymes; and (4) energy metabolism under a food-limited environment may be increased by expanded and positively selected gene enrichment in AMPK and mTOR signaling pathways. This study provides insights into the underlying genetic basis and molecular evolution of deep-sea vertebrates and provides valuable genomic resources for future investigations of deep-sea biology. Keywords: deep-sea, eels, Ilyophis, adaption, high hydrostatic pressure.