Microcystis aeruginosa is a hepatotoxin producing cyanobacteria, found globally in freshwaters. In the present study, an algicidal bacterium against M. aeruginosa was isolated from Bhimtal Lake (29°20’39”N; 79°33’32”E) of Himalayan region of Uttarakhand, India. The isolated bacterium Exiguobacterium acetylicum strainTM2was identified by morphological characteristics, biochemical characteristics and partial 16S ribosomal DNA (rDNA) gene amplification (GenBank accession number: KX155561). Efficacy of E. acetylicum TM2, and its mode of algicidal activity was evaluated against M. aeruginosa. E. acetylicum TM2 showed intense anti-cyanobacterial effect against M. aeruginosa, and approximately 90.0 % death of M. aeruginosa cells were observed after 10 days of incubation. The bacterium attacked the M. aeruginosa cells directly by physically coming in contact and caused damaged to its membrane and internal organelles. Cell free filtrate of E. acetylicum TM2 did not exhibited algicidal activity, which indicates that mode of algicidal mechanism, is cell to cell contact, and not chemically mediated damage by algicidal compounds released from E. acetylicum TM2. Furthermore, in vitro and in vivo pathogenicity test confirm the non-virulence of E. acetylicum TM2 and so it could be potentially useful in mitigation of M. aeruginosa blooms in water.