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Two rivers in the hot desert of northwestern México have been considered as filter barriers in the distribution of mammals: Río Conchos in Chihuahua and Río Nazas in Durango.  Between both rivers, the black-tailed jackrabbit, Lepus californicus, shows significant differences in external morphological traits.  We investigated if these differences are supported by phylogenetical signals and compared them with populations living at similar latitudes in the Baja California Peninsula to determine the importance of the genetic variation caused by the rivers.  An external mophology, and a cranial geometric morphometric analysis were performed using the dorsal, ventral, and lateral views of the skull; and a genetic analysis of cytochrome b gene.  Measurements and fur color patterns of specimens from two continental groups, north of Río Conchos (NRC) and south of Río Nazas (SRN), were compared to four groups (A-D) inhabiting different latitudes of the Baja California Peninsula (BCP).  The parietal region, zygomatic arch, and auditory bullae were identified as the main cranial structures related to skull shape; however, no differences were observed in size and shape between groups.  The phylogenetic reconstruction of L. californicus showed that it is a monophyletic species, with high branch support values (100).  It is represented by two polyphyletic subclades, one with haplotypes of the SRN and NRC populations and the other with haplotypes of the BCP populations.  The average genetic distance (p-distance) and genetic differentiation (FST) between SRN and NRC were low (0.8 % and 0.09, respectively), with higher mean values between the BCP groups (1.23 % and 0.30, respectively).  The statistical parsimony network of Cyt b did not identify a clear geographic genetic structure between haplotypes of SRN and NRC and they did not share haplotypes with the BCP populations.  There are neither cranial geometric morphometric nor genetic differences between L. californicus populations related to either the rios Conchos or Nazas; thus, these rivers cannot be considered geographic barriers.  However, there are morphological differences between the populations in Chihuahua and Durango and the populations inhabiting Baja California Peninsula, which may be associated with evolutionary distance and local habitat characteristics.

Morphological and genetic variation of black-tailed jackrabbit (Lepus californicus) populations separated by rivers