Phlox pilosa ssp. sangamonensis is a state-endangered and narrowly endemic taxon only found in Champaign and Piatt counties, Illinois. Here, we present evidence of natural hybridization between Phlox divaricata ssp. laphamii and P. pilosa ssp. sangamonensis. In May 2018, we collected a putative F1 hybrid of the two taxa in a sympatric population. We screened six microsatellites developed for North American Phlox species and measured eight morphological traits to test the specimen’s hybrid status. The microsatellite data were analyzed using a Bayesian clustering technique to infer genetic groupings. The eight morphological characteristics were analyzed using principal components analysis. We also measured the flowering phenology of P. divaricata ssp. laphamii and P. pilosa ssp. sangamonensis to assess the possibility of cross pollination. Bayesian clustering and the principal components analysis indicated that the sample was a Phlox divaricata ssp. laphamii × Phlox pilosa ssp. sangamonensis. There was modest phenological overlap between the two taxa, suggesting that gene flow is possible—though likely uncommon—in sympatric populations. We then discuss the effects of this hybridization on P. pilosa ssp. sangamonensis conservation and genetic composition.