Microhylidae account for the majority of frog species on New Guinea and have evolved an extraordinarily wide range of ecological, behavioural, and morphological traits. Several species are known for their unique paternal care behaviour, which includes guarding of clutches in some and additional froglet transport in other species. We sampled 48 out of 215 New Guinean microhylid species and all but two (Mantophryne and Pherohapsis) of 18 New Guinean genera and analysed a concatenated data set of partial sequences of the mitochondrial genes 12S and 16S, which comprises 1220 aligned nucleotide positions, in order to infer the phylogenetic relationships within this diverse group of frogs. The trees do provide resolution at shallow, but not at deep branches. Monophyly is rejected for the genera Callulops, Liophryne, Austrochaperina, Copiula, and Cophixalus as currently recognized. Six clades are well supported: (1) Hylophorbus and Callulops cf. robustus, (2) its sister taxon comprising Xenorhina, Asterophrys turpicola, and Callulops except for C. cf. robustus, (3) Liophryne rhododactyla, L. dentata, Oxydactyla crassa, and Sphenophryne cornuta, (4) Copiula and Austrochaperina, (5) Barygenys exsul, Cophixalus spp., and Oreophryne, (6) Cophixalus sphagnicola, Albericus laurini, and Choerophryne. The phylogenies provide evidence for the parallel evolution of parental care modes, life styles, and morphological traits that have thus far been emphasized in recent classifications.