The first chapter of the thesis contains a mitochondrial cytochrome oxidase I (mtCOI) phylogeny of shallow-water species in the genus Ciona. The mtCOI sequences of Northeast Pacific/Mediterranean (Type A) and Northwest Atlantic (Type B) Ciona intestinalis differ by ~12% and Ciona roulei is nested within Type B. Ciona savignyi differs from all other haplotypes by 13-16%. A previously undescribed but morphologically distinct Ciona sp. found at the Banyuls-sur-Mer site was [GREATER THAN] 10% divergent from all other haplotypes. The second chapter builds upon the mtCOI phylogeny and includes six nuclear genealogies for the genus Ciona. From these genealogies, I conclude that Type A and Type B are well-supported monophyletic groups. In spite of their morphological similarity, Type A vs. Type B divergences range from 0.035 to 0.124. In contrast, the morphologically distinct C. roulei is embedded within Type B in all genealogies, and Ciona sp. appears to be associated with Type B/C. roulei to the exclusion of Type A. In the third chapter, I investigated the distribution of Type A and B in areas of potential sympatry to determine whether these two types occur together and if so, whether they show evidence of hybridization and introgression. Then I combine my data with other studies to investigate general patterns of reproductive isolation vs. divergence in marine broadcast spawners. Type A and B do occur sympatrically and their genomes show low levels of introgression. Type A and B may be near the upper limit of the range of divergence values where introgression is still possible. However, introgression at divergence levels similar to those found in Ciona does occur, prompting questions about the strength of postmating prezygotic reproductive barriers in marine broadcast spawners. In the fourth chapter, I identified three candidate sperm GRPs and used these to test whether reinforcement is occurring in this system by testing whether positive selection (as a proxy for prezygotic isolation) is stronger in sympatry than allopatry. While little evidence for reinforcement was found in these three candidate GRPs, tests such as those performed here may provide important insights into the process of speciation in marine broadcast spawners.