Occurrence of cyanobacterial blooms is becoming a global environmental issue. Next to Microcystis bloom, Anabaena bloom is also the main bloom type with more diversity in production of cyanotoxins and odour substances, and removal of Anabaena blooms is also much concerned. One strain encoded as WP with strong algicidal activity against Anabaena eucompacta CHAB 1799 was isolated from a soil environment in Wuhan city. The 16S rRNA gene sequence of the WP strain showed 99.6% similarity with that of Lysinibacillus fusiformis NRS-350. Based on morphological, physiological and molecular phylogenetic features, algicidal bacterium WP was identified as Lysinibacillus sp. Its algicidal characteristics on A. eucompacta was also tested. Lysinibacillus sp. WP lysed A. eucompacta CHAB 1799 at low cell density (6×10³ cfu/ml), and lysis effects of the Lysinibacillus sp. WP on A. eucompacta were related to growth stages of A. eucompacta CHAB 1799 rather than the growth stages of the strain WP. The strain WP lysed algae by secreting metabolites. Such results in the present study increase the resource bank of algicidal bacteria, providing more potential to treat the new type blooms such as A. eucompacta dominated bloom in China.