Shared phylogenetic breaks often are associated with clear geographic barriers but some common phylogeographic breaks may lack obvious underlying mechanisms. A phylogenetic break involving multiple taxa was found in the Baja California Peninsula that was associated with a past sea barrier. However, geological evidence is lacking for this barrier's past existence, and despite its current absence, the genetic breaks have persisted. This work explores the relationships between the current climatic niches for matrilineages of 11 vertebrate species as a possible explanation for the current geographic partitioning of matrilineages. We evaluated the climatic occupancy of each matrilineage through ecological niche models, background similarity, niche overlap, niche divergence, and Mantel tests. We found disparities in the climatic occupancy between north and south matrilineage of each taxon. Northern matrilineages are associated with lower temperatures and winter rains, while southern matrilineages reside in areas with higher temperatures and summer rains.