Eremalche parryi (Greene) Greene is an annual herb endemic to Central California, USA. It has two subspecies – parryi and kernensis – which are reported to differ in breeding system and morphology. The circumscriptions of the E. parryi subspecies have never been quantified and tested, which is of critical concern as subsp. kernensis is listed as Endangered under the Federal Endangered Species Act. Here, we present the preliminary results of a study aimed at examining the circumscriptions of the subspecies using phylogenomics and morphology. For the phylogenomic analyses, we developed and analyzed a SNP dataset for Eremalche taxa and close relatives in the Malvaceae using the reduced representation ddRADseq approach. To examine the circumscription of the subspecies using morphology, we gathered morphometric and color data from ca. 200 field-collected samples of E. parryi, focusing on taxonomically important flower features. Preliminary maximum likelihood phylogenetic analyses recover a well-supported tree. Eremalche is monophyletic with strong support. Samples of E. rotundifolia form a clade with strong support sister to all other samples of Eremalche. Samples of E. exilis and E. parryi are reciprocally monophyletic, each clade with maximum statistical support. Samples of the E. parryi subspecies are interdigitated, with support values low to moderate throughout the E. parryi clade. Morphometric analyses suggest that plants assigned to the two E. parryi subspecies are not statistically different from one another. However, it does seem clear that the pistillate flowers produced by some E. parryi plants are distinctive, with perianths smaller in all measured dimensions. Furthermore, plants of E. parryi subsp. kernensis with bisexual flowers are statistically different from subsp. parryi and pistillate-flowered subsp. kernensis in having fewer carpels. A similar pattern was reported by Bates, who suggested that plants of subsp. kernensis with bisexual flowers may have undergone a reduction in carpel number to allocate greater resources to anther/pollen production. This hypothesis – then limited to subsp. kernensis – may work equally well at the species rank in explaining the evolution of gynodioecy in E. parryi. Should our preliminary findings continue to hold in further analyses using expanded datasets, abandoning the E. parryi subspecies may be warranted.