The tadpole shrimp, Triops cancriformis (Bosc, 1801) (Branchiopoda; Notostraca), is a temporary pool specialist invertebrate native to Europe classified as endangered across its distribution. Populations are threatened by habitat destruction through land development and urbanisation. There are just two remaining populations in the UK, but traditional methods are inefficient for discovering and monitoring populations. Furthermore, the genetic relationships between both populations is unknown. This thesis focuses on the design, development and application of effective molecular methods to address the shortcomings of current methods for the detection and monitoring of T. cancriformis populations. To this end I designed a species-specific PCR assay that reliably and efficiently identified extant T. cancriformis populations and, perhaps equally importantly, determined viable egg bank densities within them. Application of this method to historic sites on the Solway Firth, south west Scotland, confirmed the species' absence. To increase the scope of experiments in molecular studies, I developed a single, modular and cost effective alternative DNA extraction method to those of the commercial kits available. To better serve the conservation of T. cancriformis, I created a highly effective process for the rapid spot testing of multiple sediment samples for viable T. cancriformis diapausing eggs. Finally, using a genomewide approach I identified and genotyped SNPs from multiple individuals (RAD-seq) to ascertain genetic diversity and population genetic structure of T. cancriformis across its European distribution. Utilising these newly developed methods I present a molecular 'toolkit' for future T. cancriformis conservation. Additionally, I add to existing evidence that T. cancriformis is indeed extinct at historic sites on the Solway Firth, Scotland. Finally, I determine that the two remaining extant populations of T. cancriformis in the UK have very little genetic diversity and are not genetically differentiated, but they are distinct from the other European populations analysed.