Abalone (Haliotis spp.) are marine broadcast spawners that inhabit temperate and tropical waters across the globe. Their importance as a fisheries resource has resulted in considerable research into key aspects of their biology, particularly around growth and reproduction. In addition, there has been ongoing interest regarding the genetic variation in both wild and hatchery populations. The majority of abalone dispersal probably occurs during a pelagic lecithotrophic larval stage. In general, oceanographic features, life history characteristics, and larval dispersal ability can manipulate dispersal and gene flow patterns of marine fauna. In the case of abalone, considerable research has examined the population genetic structure of a variety of species, and several papers implicate ocean currents and life history characteristics as important factors that define population genetic structure. In comparison to other abalone species, little information regarding the genetic structure of New Zealand's endemic H. iris exists. The goal of this thesis was to elucidate the genetic structure of H. iris using mitochondrial and nuclear markers in regards to two potential barriers to gene flow, the Cook Strait region and the gamete recognition protein, lysin. The genetic structure of H. iris was first examined in regards to a consistent pattern of genetic structure emerging in recent literature of coastal marine invertebrates around New Zealand: specifically, a north-south genetic split that occurs in the Cook Strait region (Chapter 2). Two regions of the mitochondria (totaling 1055 bp) were amplified across 477 individuals from 25 locations around New Zealand. A north-south split around the Cook Strait region was evident among H. iris samples. Unlike the other studies of New Zealand coastal marine invertebrates, the north-south split for H. iris was not located across regions of reported upwelling; instead the split was located across Cook Strait narrows. The north-south split was reflected in increased haplotype diversity for the northern samples. Genetic structure was also examined using microsatellite loci. After unsuccessful attempts at cross-species amplification using 8 loci developed for H. rubra and 11 loci developed for H. midae, 13 polymorphic loci were isolated de novo for H. iris (Chapter 3). Of these, three very polymorphic loci were optimized for population genetic analyses. These three loci were used to genotype 447–459 individuals from the same 25 locations examined with mitochondrial DNA (Chapter 4). Like the mitochondrial DNA, the microsattelites indicated population genetic structure around the Cook Strait region; however the split identified with microsatellites occurred in the greater Cook Strait region with two sample sites from the north of the South Island grouping with the North Island. Extrinsic barriers, like the Cook Strait region, are the primary focus of studies examining differentiation in marine invertebrate fauna. However, dispersal of an individual to a new population does not necessarily mean it can successfully reproduce with individuals of the new population. Potentially, populations may be diverging at genes essential for reproduction, i.e. gamete recognition proteins. The abalone egg recognition protein, lysin, is one of the best characterized gamete recognition proteins in marine broadcast spawners. Despite its well-understood function and structure, studies examining variation in lysin have been limited to small sample sizes (N ≤ 11) and have found very little variation. Here, lysin was screened across 287 individuals from 17 sampling sites around New Zealand to assess intraspecific variation and genetic structure across the Cook Strait region (Chapter 5). The majority of the variation in a 783 bp fragment spanning from exon 4 to 5, was located in the intron. The variability in this fragment detected no genetic structure among samples or across the Cook Strait region. The variation in lysin was considerably lower than the variation in either the mitochondrial DNA or the microsatellite loci. To determine whether this was an artifact of being a nuclear sequence, which, in general, have a lower mutation rates than microsatellite markers and mitochondrial DNA and a larger effective population size then mitochondrial DNA, or was a signature of a recent selective sweep, 857 bp of the Gα1 intron was assessed for genetic variation in 227 H. iris individuals from 14 sampling locations (Chapter 6). The Gα1 intron was considerably more diverse than the lysin fragment examined, suggesting that the relative lack of variation in the lysin fragment has resulted from a recent selective sweep. Additionally, the Gα1 intron was used to examine population genetic structure across the Cook Strait region and detected a weak but significant pattern of structure consistent with that detected using the microsatellite loci. Overall, the a priori tests of genetic structure based on mitochondrial DNA, microsatellite markers, and the across Gα1 intron all identified a north-south genetic split around the Cook Strait region; however, the patterns of this split was slightly inconsistent among molecular markers. When cluster analyses were applied the patterns of genetic structure became more similar: for the mitochondrial, microsatellite, and Gα1 intron data, cluster analyses indicate that only one sample from the north of the South Island groups with the North Island, while a few discrepancies existed in regards the grouping of samples from the east coast of the North Island.