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The genus Meristogenys (Anura: Ranidae), endemic to Borneo, presents serious taxonomic problems despite being one of the commonest frogs in the mountainous regions of this island. We investigated molecular and morphological variations in Meristogenys whiteheadi (Boulenger, 1887) using larval and adult specimens from Sabah and Sarawak (Malaysia). We found three allopatric lineages in this species. We regard each of these as a distinct species because they are separated by a large genetic distance, and do not form any monophyletic group. Their morphological characters indicate that the distributional range of M. whiteheadi s.s. is divided into two disjunct areas: Mt Kinabalu (northern Sabah) and northern Sarawak. The two other lineages occupy ranges between those of M. whiteheadi, and represent undescribed cryptic species. One of these, Meristogenys stigmachilus sp. nov., collected from the northern part of the Crocker Range, is distinguished from M. whiteheadi by black spots on the upper lip and dark dots scattered on the back. A second undescribed species, Meristogenys stenocephalus sp. nov., was collected mainly from the southern part of the Crocker Range, and is characterized by the large body size of males and a relatively narrow head. Meristogenys stenocephalus sp. nov. also differs from M. stigmachilus sp. nov. and M. whiteheadi in larval morphology, but larvae of the latter two cannot be differentiated morphologically. We discuss relative tibia length, a diagnostic specific characteristic in the genus Meristogenys, and the relationships between body size and sexual size dimorphism in this genus.

We identified three distinct sympatric lineages of frogs among specimens previously considered a single species (Meristogenys amoropalamus Matsui), based on 909 bp of mitochondrial DNA (12S rRNA and cytochrome b). To seek evidence of reproductive isolation between these lineages, we first analyzed a 249-bp fragment of the nuclear proopiomelanocortin (POMC) gene and found five haplotypes, of which two were limited to lineage 1 and three belonged to lineages 3 and 4. In a subsequent phylogenetic analysis of a 1313-bp fragment of nuclear POMC, Rag-1, and rhodopsin, lineage 1 was again distinct, while lineages 3 and 4 could not be differentiated. The results of the nuclear gene analyses suggest that lineage 1 is strongly isolated reproductively from lineages 3 and 4, which are not isolated from each other. This conclusion conforms to groupings based on larval morphology. These results indicate that frogs morphologically identified as M. amoropalamus should be split into two sympatric species, one of which contains two mitochondrial lineages that have presumably been retained via deep coalescence.