Abstract: Understanding how the physical environment shapes patterns of population connectivity is essential to understanding the evolution and conservation of biodiversity. While dispersal barriers that promote regional genetic differentiation are often apparent in terrestrial environments, the relationship between the physical environment and barriers to connectivity in marine populations is less obvious because most species have a dispersive pelagic larval stage capable of traversing long distances. My thesis examines how the abiotic environment shapes genetic structure and population connectivity of marine invertebrates across Indo-West Pacific using Tridacna giant clams as a model. Data from Tridacna crocea indicates strong genetic structure between West Papua, central Indonesia/Philippines, and Sumatra. The estimated average dispersal distance was far below predictions based on passive dispersal via currents and virtually zero between regions. These results indicate potent limits to genetic and demographic connectivity for this species, and are likely related to sea level fluctuations, physical oceanography and larval ecology. Results from mitochondrial DNA were consistent with those from 9 microsatellites. To evaluate the generality of this result, I compared mtDNA phylogeographic patterns in Tridacna crocea, T. maxima, and T. squamosa. Concordant patterns across three congeners suggest the influence of broadly acting oceanographic and/or geological forces in shaping regional genetic structure. Patterns are concordant with a recent global classification of marine environments, suggesting that abiotic processes are structuring marine biodiversity at multiple levels. Finally, I examined the symbiosis between giant clams and their algal symbionts. Results show that symbiont types differ with temperature and that symbiont communities may differ between individuals based on local environmental conditions. Given the well-documented ecological differences among symbionts, these results highlight potential ecological consequences of this symbiosis in the face of global climate change. Combined, these results indicate that patterns of regional divergence are shaped by physical oceanographic and geological processes, but may also be shaped by clam-algal symbiosis. These data have strong conservation implications. Understanding the scale and pattern of population connectivity is critical to effective conservation planning, and the variation of symbiont communities with temperature may prove useful in managing populations of these endangered species in periods of rising ocean temperatures.