The southeastern azaleas (genus Rhododendron, section Pentanthera) are a complex group of species that show evidence of rapid diversification and widespread hybridization. Species within the clade often have substantial morphological overlap but also show evidence of morphological differentiation and geographic separation along temperature gradients. To understand speciation in the southeastern azaleas, more genetic resources must be developed for phylogenetic and population genetic analyses. The objective of this study was to identify single nucleotide polymorphisms (SNPs) in R. prunifolium from sequence data. We isolated DNA from thirteen R. prunifolium individuals using a modified CTAB protocol followed by bead clean-up. We then prepared sequencing libraries for paired-end read sequencing using the Illumina method. Here we report the results of the sequence analysis and genetic marker identification.