The analysis of 9 populations ofEcheandia nanashowed all to be diploid,with2n= 16, n −. 8 (x = 8). The analyzed populations displayed two cytotypes.Cytotype A − 10m+6sm, having two pairs of chromosomes with a satellite, was observed in four populations from the eastern flanks of the Pachuca mountain range. The five remaining populations from the western flank of the Pachuca and Sierra Nevada mountain ranges (Mexico) showed cytotype B + 6m+8sm+2st, having one pair of chromosomes with a satellite. The analysis of meiosis revealed heterozygotic exchanges. Analysis of MI showed three heteromorphic bivalents in cytotypes A and B. Analysis of AI showed sub-chromatid aberrations, (side arm bridges = SAB), which were more frequent in cytotype B (39.88+44.84%) than in cytotype A (2.86+31+53%). Cells with two bridges (SAB aberrations) were observed in cytotype B.The intraspecific cytological and genical differentiation of cytotypes A and B is probably the result of geographical isolation between populations of E. nana. This suggests that this species is undergoing through a major process of genomic differentiation involving heterozygotic chromosomal rearrangements; which favors a process of speciation between both cytotypes without the occurrence of significant morphological changes. This cytological and genical differentiation between cytotypes A and B was evident in the significant differences of the low number of fruits and viable seeds produced after cross-pollination among cytotypes (AxB: 0–16 fruits; 0–448 abortive seeds), relative to the larger values recorded after crosspollination within cytotypes (AxA: 4–48; 152–1824) (BxB: 3–89; 14–3382).