Root-knot nematodes (RKNs) can infect almost all crops and cause huge economic losses in agriculture worldwide. An in-depth understanding of bacteria with nematicidal activity is essential for an effective and environmentally friendly control of RKNs. Fictibacillus arsenicus G25-54, a gram-positive and spore-forming bacterium isolated from a submerged sand bank, shows nematicidal activity against free-living Caenorhabditis elegans and RKNs. Here, we report the complete genome of F. arsenicus G25-54, which contains a circular chromosome and encodes ten potential nematicidal factors with twelve secondary metabolite gene clusters. Additionally, it encodes five arsenic resistance and transformation related proteins, which may provide the potential arsenic-resistance activity.