Two members of the family Flavobacteriaceae were isolated from subseafloor sediments using artificial seawater with cellulose, xylan, and chitin as the sole carbon and energy sources. Here, we present the complete genome sequences of Krokinobacter sp. strain 4H-3-7-5 and Lacinutrix sp. strain 5H-3-7-4, which both encode putatively novel enzymes involved in cellulose, hemicellulose, and chitin metabolism.Members of the family Flavobacteriaceae are well known for degrading complex polymeric substrates in marine habitats (4). Two marine representatives of this family, Krokinobacter sp. strain 4H-3-7-5 and Lacinutrix sp. strain 5H-3-7-4, were isolated from subseafloor sediments at Suruga Bay (Japan) at depths of 31.4 and 41 m using a mixture of cellulose, xylan, and chitin as the sole carbon sources in enrichment cultures.To gain insight into the gene repertoire of these organisms, the complete genomes of Krokinobacter sp. strain 4H-3-7-5 and Lacinutrix sp. strain 5H-3-7-4 were generated at the Department of Energy (DOE) Joint Genome Institute (JGI) using Illumina (1) and 454 (3) technologies. For Krokinobacter sp. strain 4H-3-7-5, we sequenced an Illumina GAii shotgun library, which generated 38,286,828 reads (2,909 Mbp); a 454 Titanium standard library, which generated 205,742 reads; and a paired-end 454 library (average insert size, 11.1 Ϯ 2.8 kbp), which generated 287,950 reads, totaling 136.6 Mbp of 454 data. For Lacinutrix sp. strain 5H-3-7-4, we sequenced an Illumina GAii shotgun library, which generated 54,815,066 reads (4,165.9 Mbp); a 454 Titanium standard library, which generated 268,763 reads; and one paired-end 454 library with an average insert size of 17 kb, which generated 220,650 reads, totaling 152.2 Mbp of 454 data. All general aspects of library construction and sequencing can be found at http://www.jgi.doe.gov/. The 454 Titanium standard data and the 454 paired-end data were assembled using Newbler version 2.3, while the Illumina sequencing data were assembled with Velvet versions 0.7.63 and 1.0.13 (5).