Based on sequences of three mitochondrial and two nuclear-encoded genes, we examine genetic variation in the leaf tailed geckos Uroplatus sameiti and U. sikorae, and morphological and chromatic characteristics of the genetic clusters identified. The mitochondrial phylogeny reveals a puzzling diversity of 16 deep lineages (4 in U. sameiti and 12 in U. sikorae) differing by 2.9–9.9% uncorrected pairwise distance in a fragment of the 16S rRNA gene. Populations from Analalava in the North and Zahamena in the Northern Central East form two mitochondrial lineages clustering with U. sameiti but being deeply divergent (>8% 16S distance); however, no information on their morphology is available. In U. sikorae, the mitochondrial lineages identified form several major geographic clades, two of which (from the northernmost and southernmost populations, respectively) received substantial support in the phylogenetic analysis. No instance of sympatry of two or more mitochondrial lineages was observed, precluding an unambiguous assessment of species status under the biological species criterion without experimental approaches or detailed hybrid zone analyses. In the fragment of the nuclear encoded gene SACS we observed haplotype sharing between species and mitochondrial lineages, while in the fragment of KIAA1239 no haplotype sharing was detected although neither species nor mitochondrial lineages formed coherent phylogroups in the respective network. A screening of colour patterns from live photos, partly of the genotyped individuals, confirmed a large variation within species and populations, with a possible sexual dichromatism where a longitudinally striped phenotype is restricted to males. All individuals from populations of the U. sikorae clade from the Southern Central East and South East had an unpigmented oral mucosa just like U. sameiti, while all other U. sikorae populations are characterized by a black oral mucosa pigmentation. The extremely strong phylogeographic structure in the U. sikorae complex without obvious species-level divergences is unprecedented for large-sized squamates in Madagascar and calls for further taxonomic scrutiny using phylogenomic approaches; and it exemplifies how the loss of any major block of the remaining rainforests in Madagascar will inevitably lead to a substantial loss of genetic diversity – even if often intraspecific – in rainforest-specialized species.