Speciation involves the establishment of reproductive isolating barriers between diverging populations. Two closely related iris species, Iris atrofusca and Iris mariae, have non-overlapping geographical distributions characterized by differences in soil type and precipitation. We aimed to obtain a better understanding of pre- and postzygotic isolating barriers between these two species and the possible role of habitat-specific selection in preventing gene flow between them. We examined molecular genetic (AFLP) and phenotypic divergence and conducted species distribution modelling, tests for local adaptation and crossing experiments on the two species. The two species were found to beclearly divergent genetically and phenotypically from each other. Species distribution modelling further showed that each species distribution was largely associated with climate and soil type and that the area predicted to be shared by both species was very narrow, resulting in very high estimates of ecogeographical isolation. In contrast, other isolating barriers examined were either weak (flowering time differences) or absent (related to immigrant inviability and reduced fitness of hybrids generated from reciprocal crosses). Each species showed no home advantage in a reciprocal transplant analysis and little preference for indigenous soil type and water regime in experimental tests of this, thus indicating an absence of local adaptation. Reproductive isolation between the two iris species appears almost entirely attributable to geographical isolation unlinked to local adaptation. However, more detailed studies are required before local adaptation is dismissed as a cause of species divergence and occupation of contrasting habitats.