Freshwater bacterioplankton of the genus Limnohabitans represent a dominant group that has worldwide distribution. Here, we report the complete genome sequences of three Limnohabitans sp. (Lhab-A3 tribe) strains, i.e., INBF002, TEGF004, and MORI2, which were isolated from surface water samples from two shallow eutrophic lakes and a river in Japan.