Dendroctonus mexicanus is an endemic, generalist species of recent origin in Mexico with a wide geographical distribution. This study examined organization of the genetic variation in mtDNA to test the hypothesis that generalist species describes a poorly defined genetic structure pattern. Additionally, using nested clade analysis we investigate the historical or demographic events that might have shaped the distribution of mtDNA haplotypes. Analysis of the mitochondrial cytocrome oxidase I gene (mtCOI) sequences of 176 individuals from 25 geographical populations shows that the estimated nucleotide and haplotypic divergences were π=0.011 ± 0.003 and h=0.862, respectively. AMOVA showed that 84.7% of the genetic variation occurred within populations and 12.6% corresponded to shared variations among them. Average gene flow (Nm) estimated for all populations was 3.2. Regression between φ_ST and the natural logarithm of the paired geographical distances described a panmictic model. The nested clades analysis indicate that the general phylogeographic pattern of D. mexicanus in Mexico can be explained by a continuous dispersion event. However, the relationships among the lineages from the Sierra Madre del Sur and the rest of the mountain ranges of the country rely on an allopatric fragmentation event, and that the lineages from the Sierra Madre Occidental and the Trans-Mexican Volcanic Belt rely on long distance colonization. Based on the nested clade analysis we hypothesize a fragmentation event in the past as a result of recent dispersion events which in some cases appear to be coupled with the geological history of the mountain range systems.