Petunia hybrida (petunia) is one of the most economically important annual bedding plants in the United States. Genomic resources for petunia are lacking. Utilizing RNA-seq, de novo transcriptome assemblies were generated for the progenitor species of cultivated petunia, Petunia axillaris and P. integrifolia, and for P. exserta, a rare species that has been utilized in petunia breeding and as a model to understand pollination syndrome. Transcripts were derived from five tissue types: seedlings, callus, mixed floral developmental stages, shoot apices and trichomes. The transcriptome assemblies are being utilized for molecular marker development and gene discovery for traits of interest in Petunia.