Ophrys is amongst the best known orchid genera and is an established system for the study of pollinator-mediated floral evolution. Two species, Ophrys fusca s.l. and Ophrys dyris (= O. omegaifera subsp. dyris) belonging to Ophrys section Pseudophrys are the focus of this study. In the context of an integrative study of morphological and genetic diversity of O. fusca and O. dyris, genome size (GS) and cytotype diversity were surveyed from Portuguese populations. Flow cytometry methods were used to assess GS, and subsequently determine the ploidy level of 67 specimens, including the species and putative hybrids. Cytotypes were also confirmed based on chromosome counts from the roots of two specimens, one of each species. Constancy of nuclear DNA content (1C = 11.19 pg) and ploidy level (2n = 4x = 72, 74) was documented among all the individuals analysed. Implications are considered, in terms of interpreting the origin and predicting the persistence of putative hybrids.