Clonostachys rosea strains ACM941 and 88-710 are beneficial microbes recognized for their plant disease control and growth promotion properties, respectively. In addition to their geographical and functional overlap, the two strains also share a high degree of genetic similarity. Toward identifying the subtle differences that underlie their strain specific applications, their genomic sequence is reported here. These genomic sequences form a foundation for future studies aimed at identifying the genomic and metabolic machinery driving their respective beneficial properties.