Hybridization is a source of genetic diversity whose frequency and ecological importance is increasingly clear. However, the importance of hybridization in microbial eukaryotes is relatively unknown due to issues such as lack of sampling or difficulty in detection. Prymnesium parvum (Haptophyta) is a cryptic species complex of toxic microalgae with member species that form ecosystem disruptive blooms around the world. Two closely related clades within the species complex have been reported to form hybrids, but this observation has been disputed. We screened 27 strains of P. parvum for signatures of hybridization. A SNP based evolutionary analysis identified 4 clades including a hybrid clade containing 13 strains found in inland Texas and along the eastern coast of the United States. Single cell re-isolates of two strains in this hybrid clade further confirmed that this signature is due to contamination and not contamination. Identified hybrids form five distinct subclades that can be differentiated based on unique patterns of parental SNP retention. Additionally, a new clade of P. parvum was discovered in Japanese waters. This supports the existence of a hybrid genotype in North American waters and a sexual stage to the P. parvum lifecycle, and expands the cryptic diversity present in the P. parvum species complex.