The 9 km² uplifted lagoon of Taiaro Atoll (15°45′S, 144°38′W) is hypersaline due to its isolation from the ocean, yet it contains a high diversity of fish. The question unifying our expedition was to discover whether these assemblages could be self-sustaining despite very limited contact with the ocean. Although we were constrained by time, collections of fish larvae showed that some species can complete their life-cycle within the lagoon, while others differed genetically between the lagoon and the ocean, consistent with restricted gene flow. The lagoon contained few oceanic species of zooplankton, confirming its general isolation, but nevertheless some fish species may depend upon infrequent colonisation from the ocean (when large waves drive water over the normally dry reef crest). Isotopic signatures in fish otoliths suggest the basis for a more definitive and inclusive test of the sources of the lagoonal assemblage.