Latitudinal gradients exhibit environmental and geographic factors determining the distribution of biodiversity. They are expected to influence speciation, but evidence on this process is scarce. We evaluated the genetic and environmental variation between Dioon sonorense and D. vovidesii, two cycads from Mexico, to reveal the factors involved in their divergence. Using genome-wide loci, we estimated the species delimitation, gene flow, and compared multiple scenarios of divergence. We estimated the variation of climate among populations and used ecological niche models to test niche overlap. The effect of climate on the genetic variation among populations was evaluated using linear models. Our results suggest that an ancestral population split into the two species ~829 ky ago. The delimitation along the latitudinal gradient occurs due to a sharp zonation of environmental seasonality. The northern species, occurs in seasonal climates but retains the same niche of the southern species. However, the genetic variation cannot be solely explained by stochastic processes; the latitudinal-associated seasonality has been an additive factor that in the divergence. The parapatric speciation model can explain the origin of this species pair. This study represents an example of how speciation can be achieved by the effect of the latitudinal variation among populations.