Seagrasses are ephemeral, patchy habitats, under increasing risk of fragmentation due to anthropogenic changes. The ongoing and increasing loss of seagrass makes it essential that we understand the processes of movement and connectivity of the animals which rely on seagrass as a habitat. Shrimp are among the most abundant and diverse animals in seagrass habitats. Much of the published literature remains focused on one particular facet of shrimp life. Ecologists tend to generalise habitat-scale patterns of shrimp family groups where more specific studies on individual species may only focus on the biology, taxonomy or phylogeography alone. Few studies combine ecology, biology and phylogeography. This thesis attempts to achieve a comprehensive understanding of the biology, ecology, diversity, distribution, connectivity, and phylogeography of one of the most abundant shrimp taxa from Queensland seagrasses: Phycomenes zostericola. This holistic approach provides a solid foundation of information against which to compare future connectivity studies and also other seagrass species. In general, caridean shrimp are planktonic during their early life stages and will then recruit into the same habitat type which their parents occupy. Having a planktonic larval phase allows them the potential for broad dispersal. This study found that the potential for movement among P. zostericola populations is considerable; the adults were found to frequently move among seagrass patches and larvae have a planktonic phase of anywhere up to three weeks. Surprisingly, P. zostericola show a surprising amount of genetic structure for a marine species with a planktonic larval phase. The close association of adults to seagrass habitat and the reliance of P. zostericola larvae on a current to maintain suspension may be the limiting factors preventing P. zostericola from fulfilling their migration and dispersal potential. P. zostericola has a broad distribution and can be found in most seagrass habitats around Queensland. A cryptic (morphologically indistinguishable) sibling species was discovered that is sympatric throughout the northern range of the P. zostericola distribution. The discovery of the divergent taxon provided a unique opportunity for a comparative phylogeographic study. The two sibling taxa diverged between 3.2 and 4.6 million years ago and since then have been exposed to similar biogeographic influences. A mitochondrial dataset, using the gene cytochrome oxidase I (COI), describes the historical and contemporary levels of connectivity and demographic change in response to marine biogeographic boundaries, sea level changes and currents. While regional 3 genetic structure was found to be similar between the two species, demographic changes were not. The two populations of Phycomenes are also under some kind of north vs. south selective pressures. The nuclear gene, myosin heavy chain (MyHC), shows a distinct latitudinal pattern in both Phycomenes species. This genetic pattern indicates that groups north and south of far northeast Queensland are exposed to significantly different conditions resulting in different selective forces operating on the myosin gene. Both the mitochondrial gene COI and the nuclear gene MyHC were analysed for broadly distributed populations of two other seagrass caridean species; Latreutes mucronatus and Cuapetes sp. Similar to Phycomenes, both of these species contained multiple, morphologically identical, yet genetically distinct species. The deep levels of divergence indicate that speciation had occurred between 8 and 25 million years ago. The multiple cryptic taxa found in this study confirm two commonly stated hypotheses about marine taxa: firstly, cryptic speciation is common in marine taxa and this is just as true for seagrass caridean shrimp as other groups. Secondly, biodiversity estimates in shallow marine systems are currently underestimated due to high levels of unidentified cryptic taxa. A loss of statistical power is unavoidable in sampled populations which contain cryptic taxa. Although small sample numbers of Latreutes and Cuapetes species did not allow rigorous genetic statistical analysis they did provide some insight into the structure of these populations. All analysed seagrass shrimp taxa (Phycomenes, Latreutes and Cuapetes) maintained signals of demographic expansions prior to the last glacial maximum, suggesting that the vast and rapidly changing sea-levels throughout the Pleistocene did not have drastic demographic impacts on seagrass shrimp populations over broad spatial scales. Although lowered sea levels did not have dramatic demographic effects, low sea levels and strong currents probably provided the necessary conditions for long distance migration / dispersal events; this is evident in the haplotype sharing between geographically distant populations for most of the study taxa. This study provides valuable insight into the contemporary levels of connectivity and the past responses to major environmental and habitat changes. These data will hopefully contribute to the much needed baseline data used to guide future conservation efforts of inshore marine habitats.