Niche conservatism is the tendency of lineages to retain the same niche of their ancestors. It constrains biological groups and prevents ecological divergence. However, the theory predicts that niche conservatism can also prevent gene flow, strengthen drift and increase local adaptation: does it mean that it can facilitate speciation? Why does this happen? This study aims to respond to these questions. We examined the variation of the chloroplast DNA, genome-wide single nucleotide polymorphisms, morphological traits, and environmental variables across Dioon merolae cycad populations. We tested geographic structure, scenarios of demographic history, and niche conservatism between geographic groups. Lineage divergence is associated with the presence of a geographic barrier consisted of unsuitable habitats for cycads. There is a clear genetic and morphological distinction between the geographic groups, suggesting allopatric speciation. However, even in contrasting available environmental conditions, groups retain the same ancestral niche, suggesting niche conservatism. Niche conservatism is a process that can promote speciation. In D. merolae, lineage divergence occurred because unsuitable habitats represent barrier against gene flow, facilitating that population groups experience isolated demographic histories and disparate environmental conditions. This empirical case explains why cycads, despite their biological stasis, could recently diversify into the modern ecosystems worldwide.