The northwestern Mexican Baja California state is an ecologically unique area being the only part of the country with a Mediterranean ecosystem and a high species diversity and endemism for many groups. Studies on the biodiversity of the region are scarce, especially regarding ecologically important groups such as terrestrial arthropods. Even scarcer are studies on another important aspect of diversity, namely genetic diversity. Due to the paucity of information, the genetic diversity and population histories of the 2 most abundant species of Phidippus (Araneae: Salticidae) of the region are presented, based on nuclear and mitochondrial DNA data. Phidippus johnsoni, the more widespread of the 2, belonged to 1 large, panmictic population in Baja California, while P. phoenix was divided into 2 populations. Both species have high genetic diversity and estimated large population sizes, which increased during the last 150,000 years for P. johnsoni, and the last 30,000 years, after the Last Glacial Maximum for P. phoenix. This study, therefore, reinforces the importance of this area, not only for its species diversity but also for the genetic diversity found within the populations, which reflects ecological stability during the Pleistocene, allowing for the accumulation of genetic diversity through time.