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Niche conservatism theory suggests that recently diverged sister species share the same ecological niche. However, if the ecological niche evolves as part of the speciation process, the ecological pattern could be useful for recognizing cryptic species. In a broad sense systematists agree that the niche characters could be used for species differentiation. However, to date such characters have been ignored. We used the genetic algorithm for rule-set production for modelling the ecological niche as a means of inferring ecological divergence in allopatric populations of muroid rodents for which taxonomic identity is uncertain. Our results show that niche differentiation is significant in most of the identified phylogroups. The differentiation is likely associated with natural evolutionary units, which can be identified by applying species concepts based on phylogenetic and ecological patterns (e.g. phylogenetic, cohesive, evolutionary). Even so, the role of the niche partition within phylogenetic reconstruction may be a limited one.