The extent of chromosome structural differences such as permanent translocations and paracentric inversions has been studied in the hybrid complex of Phlomis composita and its putative parental taxa P. lychnitis and P. crinita. They are detected as meiotic abnormalities during microsporogenesis. In total, 117 plants from 19 populations in Andalusia (southern Spain) and Levante (eastern Spain) were studied for ploidy level, chromosome clumping, multivalent or univalent formation, late bivalent disjunction with bridges, chromatin bridges and fragments, irregular polysporads and variable pollen size. All individuals had the diploid chromosome number 2n = 20, with no significant difference in the frequencies of the above meiotic abnormalities either at taxon or population levels. However, very different frequencies were observed on the regional scale between populations in Andalusia and Levante. The results are discussed within the theoretical framework of homoploid hybrid or recombinational speciation.