Complete genome sequence of Sphingorhabdus sp. M41, a versatile hydrocarbon degrader, isolated from crude oil-contaminated costal sediment

•Sphingorhabdus sp. M41 has a versatile hydrocarbon-degrading capability.•Complete genome of strain M41 was sequenced.•The genome contains genes encoding various oxygenases, catalyzing oxidation of aromatic and aliphatic hydrocarbons.•The genome information will provide insights into the bioremediation of crude oil-contaminated costal sediment. Sphingorhabdus sp. M41, capable of degrading aliphatic and aromatic hydrocarbons, was isolated from crude oil-contaminated costal sediment by an enrichment culture and its complete genome was sequenced. The genome of strain M41 has a chromosome with a size of 3,324,420bp, including 44 tRNAs, 6 rRNAs, and 3118 protein-coding genes. In addition, many potential genes responsible for the biodegradation of aliphatic and aromatic hydrocarbons were identified from the genome. This is the first complete genome of the genus Sphingorhabdus, which will provide insights into the bioremediation of crude oil-contaminated costal sediment by strain M41.