Two members of the family Flavobacteriaceae were isolated from subseafloor sediments using artificial seawater with cellulose, xylan and chitin as sole carbon and energy sources. Here, we present the complete genome sequences of Krokinobacter sp. 4H-3-7-5 and Lacinutrix sp. 5H-3-7-4 which both encode for putatively novel enzymes involved in cellulose, hemicellulose and chitin metabolism.