Prymnesium parvum is a unicellular, biflagellated alga in the lineage Haptophyta. P. parvum forms toxic blooms around the world, which are very disruptive to local ecosystems. In the United States, the first documented bloom of P. parvum occurred in the Pecos River of Texas in 1985. Since then, the frequency and intensity of P. parvum seasonal blooms have increased and spread from the American Southwest to freshwater systems as far north as Ohio River tributaries. Recently, P. parvum has been characterized as a cryptic species complex consisting of at least three member species. These member species are referred to as A-, B-, and C-types based on their unique chemotypes. Previously, all known strains of P. parvum from Texas were characterized as A-types. However, the genetic diversity of Texas P. parvum is not well understood outside of a handful of isolated strains. From Winter 2018 to Sumer 2020, we isolated an additional 35 P. parvum strains from eight separate bloom events in Central and Western Texas. The genomes of these newly isolated strains were sequenced using Illumina, and all strains were characterized in terms of their genome size, heterozygosity, and ploidy. We performed a comparative phylogenomic analysis that included a total of 56 P.parvum genomes from Texas and around the world. Our analysis uncovered the first known occurrence of B-type P.parvum in Texas. Moreover, we found that A-type and B-type species of P. parvum co-occur in Texas blooms. Texas A-type strains showed significant intraspecific genetic variation, with haploids, diploids, and hybrids strains identified. In contrast, all B-type strains were diploids and showed limited sequence level divergence. Overall, this analysis reveals significant genetic diversity within Texas blooms of P. parvum. Future work is needed to integrate these results with behavioral and metabolic differences between the two cryptic species and to determine the relative impact of both species to ongoing blooms in Texas.