Phylogenetic relationships within the genus Leptolalax have been insufficiently resolved, while the relationships of a related genus Leptobrachella with other genera are totally unknown. In order to improve these situations, we assessed the phylogenetic relationships among 19 species of Leptolalax and four species of Leptobrachella based on 2067–2527 bp sequences of the mitochondrial 12S and 16S rRNA genes using maximum likelihood and Bayesian inference methods. Leptolalax and Leptobrachella formed a clade, in which each of the Bornean Leptolalax, continental Leptolalax, and Leptobrachella formed a clade with unresolved relationships. Within the continental clade, the species from the Malay Peninsula formed a sister clade to the clade of the remaining regions. The species from southern Thailand formed a sister clade to the species from more northern regions. These results suggest confining the name Leptolalax to Bornean species, and reexamining the contents of the name Lalos currently recognized. Pointed digital tips unique to Leptobrachella might have arisen parallelly in ancestral Leptolalax as in Leptobrachium. Absence of species common to both Borneo and the neighboring continent in Leptolalax unlike in many other anuran genera occurring in Borneo, suggests a unique evolutional history of the genus.