Context. The phylogenetic diversity and biogeography of most animal and plant lineages endemic to the Australian Monsoonal tropics remains poorly understood. Of particular note (and in contrast to many other tropical regions in both Australia and elsewhere) is the current paucity of evidence for diverse endemic radiations of restricted-range taxa.

Aims . To use recently collected material from major surveys of the Kimberley Islands, Western Australia, to expand on a previous study that provided preliminary evidence of very high levels of geographically structured phylogenetic diversity in a lineage of tiny geckos (Crenadactylus).

Methods . Mitochondrial (ND2) and nuclear (RAG-1) sequence data were used to estimate the relationships, phylogenetic diversity and timescale of diversification of all populations of Crenadactylus from northern Australia from which samples for genetic analysis were available.

Key results . In striking contrast to the two subspecies currently recognised in the Kimberley, our analyses confirm the existence of a notable diversity of highly divergent and apparently allopatric lineages within the Kimberley, including at least 10 that are estimated to date to the late Pliocene/early Miocene (or earlier) and seven that we recognise as candidate new species. Most of this diversity is concentrated in the high-rainfall zone along the western edge of the Kimberley.

Key conclusions . A growing number of genetic datasets are revealing northern Australian vertebrate clades characterised by the juxtaposition of deeply divergent and highly geographically structured genetic diversity on the one hand, and major geographic gaps in sampling that impede full assessment of the distribution and taxonomic significance of this diversity on the other.

Implications . There is a pressing need for further surveys, voucher material and phylogenetic analyses to allow us to properly understand the diversity, biogeography and conservation needs of the northern Australian biota.