The origins of biodiversity have intrigued evolutionary biologists since the earliest times, and have resulted in a plethora of theories to explain these origins. To date, there has been a tendency to use distribution patterns of biota to confirm preferred hypotheses (a field known broadly as historical biogeography), instead of a genuine attempt to test between competing hypotheses.A recently emerging field utilises the ease with which DNA sequences can be read to provide more objective testing of hypotheses; an approach referred to as 'comparative phylogeography'. Here we advocate the use of a novel replicated approach to distinguish between sets of alternative hypotheses as a route towards testing the major theories.A number of theories have been put forward for diversification in one of the global 'hotspots', the archipelagos of South-East Asia, although a general theory has yet to emerge. This region of high species richness allows for a replicated sampling of taxa to infer general biogeographic pattern s. Our approach aims to examine phylogenetic and population genetic patterns in multiple co-distributed freshwater taxa from the region, to enable us to test between competing hypotheses of diversification.Freshwater taxa are ideal model organisms for such an approach as they reflect well the underlying geological history of a given region, due to limited dispersal abilities to cross marine environments between land-masses. A further aim of the present study is to contribute towards documenting the rapidly declining biodiversity of SE Asia, which is a high priority in global conservation at present.Findings will provide a case study both for the experimental analysis of trends in biodiversity and the use of such data in biodiversity conservation- two issues of high applicability to other geographic regions, especially in those subjected to major anthropogenic impacts.