In order to ensure crew safety and understand bacterial dynamics in space habitation environments, microbial monitoring is required. We have been continuously performing microbial monitoring in the Japanese Experiment Module “Kibo” on the International Space Station in cooperation with Japan Aerospace Exploration Agency (JAXA) since 2009 (research title: “Microbe”). As of now, sampling was performed on Sep. 2009 (Microbe-I), Oct. 2010 (Microbe-IIA), Feb. 2011 (Microbe-IIB) and Oct. 2012 (Microbe-III). In this study, abundance and phylogenetic affiliation of bacteria on interior surfaces in the ISS-Kibo were determined by quantitative PCR and amplicon sequencing with a high-throughput sequencer, respectively. The surface of CBEF (incubator), inside of the door of CBEF, laptop palm rest, air intake, and handrail were selected as sampling sites. We used a new device for sampling, the microbe-collecting adhesive sheet, developed in our laboratory. According to phylogenetic affiliation of bacteria, bacteria in the phyla Firmicutes were frequently detected on the interior surfaces in the ISS-Kibo. Especially, genus Staphylococcus, which is a part of human skin microbiota, was frequently detected; thus, bacterial cells found in the ISS-Kibo might be transferred to the surfaces in the ISS-Kibo via astronauts. Bacterial number at each site was equivalent to or less than the quantification limit (10³ cells/cm² for quantitative PCR) in Microbe-IIB and Microbe-III. Previously we reported that bacterial number on various surfaces in our laboratory were around 10⁵ cells/cm². From these aspects of bacterial abundance and their phylogenetic affiliation, the ISS-Kibo has been microbiologically well maintained; however, bacterial abundance was more than 10⁷ cells/cm² at one sampling site in Microbe-IIA and microbial abundance in the ISS-Kibo may increase with prolonged stay of the astronauts. Continuous microbial monitoring is therefore important.