The fungus Calonectria ilicicola (anamorph Cylindrocladium parasiticum) is an important plant pathogen causing Cylindrocladium black rot (CBR) on peanut and Red crown rot (RCR) on soybean. CBR infection of peanuts cause symptoms such as chlorosis of leaves, blackening of taproots, and wilting, while RCR infection of soybeans lead to root and interveinal necrosis of soybean. In the present study, we sequenced the genome of four CBR-related Ca. ilicicola strains and three RCR-related Ca. ilicicola strains. The draft genome of Ca. ilicicola, ranged from 68.63 Mb to 70.35 Mb in genome size, containing 18536 to 19361 protein-coding genes. The described genome sequences will provide insights into factors that contribute to pathogenicity toward peanut and soybean and will be useful for future research in population genomics and molecular diagnostic marker development to quickly detect this pathogen.