Abstract
The first objective of this dissertation was to incorporate phylogenetic analysis to anaspidean systematics using the available morphological data. Cladistic analysis agreed with the current taxonomic classifications based on morphology, and resolved the placement of Akera within the Anaspidea. When compared to a molecular phylogeny derived from mitochondrial DNA genes (12S, 16S) the taxonomic subdivisions into the Longicommissurata and Brevicommissurata were not apparent monophyletic clades. More specifically, the genus Notarchus (a Brevicommissurata) appeared as a basal taxon related to Dolabella and Aplysia rather than to the rest of the Brevicommissurata. Morphological homoplasy, especially of the nervous system, was invoked as a possible explanation for the conflicting topologies.The molecular analysis of the genus Aplysia was in agreement with the classification proposed by Eales (1960). The evolution of inking behavior in this genus appeared to have a phylogenetic component. The subgenus Aplysia was a monophyletic clade that has lost the ability to release the purple ink.The primary purpose of the population genetics project was to study the genetic population structure of the California sea hare (Aplysia californica: Cooper) by means of molecular markers. The information obtained from this project was used: (1) to determine if any pattern of population genetic structure was due to geographic isolation between Pacific coast and Gulf of California populations, and (2) to develop polymorphic markers for aquaculture management. No signs of population structure were detected in this species by nuclear or mitochondrial markers. The genetic evidence suggested high levels of gene flow ($\sim$17 migrants per generation) between all the localities sampled. This high gene flow is probably associated with the surface circulation of both the North Eastern Pacific and the Gulf of California.