The trapdoor spider genus Aliatypus (Mygalomorphae, Antrodiaetidae) encompasses twelve described species, eleven of which are endemic to California. Several Aliatypus species show disjunct distributional patterns in California (some are found on both sides of the vast Central Valley), and the genus as a whole occupies an impressive variety of habitats. Chapter One uses molecular phylogenetics to explore the systematics and evolution of this group of spiders. DNA sequence data were collected from seven gene regions. Bayesian inference (in individual gene tree and species tree approaches) recovered a general "3 clade" structure for the genus (A. gulosus, californicus group, erebus group), with three other phylogenetically isolated species differing slightly in position across different phylogenetic analyses. For multiple species spanning the Central Valley, explicit hypothesis testing suggests a lack of monophyly for regional populations (e.g., western Coast Range populations). In addition, phylogenetic evidence clearly shows that syntopy is restricted to distant phylogenetic relatives, consistent with ecological niche conservatism. Overall, Chapter One provides fundamental insight into a radiation of trapdoor spiders found in the biodiversity hotspot of California. Chapter Two focuses on evolutionary dynamics and possible cryptic species within the nominal taxon A. thompsoni. This species was described using morphology, ecology, and behavioral traits, although molecular data in Chapter One suggests a species complex comprised of multiple cryptic species. A comprehensive sampling effort throughout the geographic distribution of this species, combined with sampling of four independent molecular markers, confirms the species complex hypothesis. These data are used in combination with multiple coalescent-based approaches to understand species limits and interrelationships within A. thompsoni. Data and analyses support a three species complex, although this is likely a conservative estimate, with potentially up to five species. Chapter Two provides a framework for determining species limits through statistical tests and analyses.