Here we have used next-generation Illumina sequencing to generate transcriptomes of four S. latifolia individuals from two morphologically divergent populations from disparate habitats, including including two females from Xativa, Spain and two males from Zagreb, Croatia. Spanish plants experience a much hotter, drier climate than Croatian plants, and the populations have ecologically relevant differences in floral and leaf characteristics (e.g., Spain has thicker leaves and produces fewer, larger flowers in comparison) (data not shown). This transcriptome data will provide population-specific SNPs for planned QTL studies using these populations to connect phenotypic diversity with the underlying genetic architecture. This transcriptome resource will also contribute to a growing set of genomics resources for S. latifolia.