Molecular genetic sequence variation of northern and northwestern mouse lemurs (Microcebus) was examined during a phylogenetic analysis of mitochondrial DNA (mtDNA) sequence data (c. 3,000 bp) for the entire genus. Phylogenetic inference of the mitochondrial DNA sequence data was generated from 132 individuals, representing 15 species of mouse lemurs. The database distinguished the 15 described Microcebus species and also provided diagnostic evidence for two further species. A comparison of the data for two mouse lemur species described from Nosy Be confirmed the existence of just one for this island population. The localities of the newly identified species are within the distributions previously recognized for Microcebus sambiranensis and Microcebus tavaratra. Formal descriptions, drawn from molecular genetic data, are presented for the two newly named species: one from Antafondro Classified Forest and the other from Montagne d'Ambre National Park. We revise the Inter-River-System hypothesis concerning the biogeographic patterns of the distributions of the northern and northwestern mouse lemurs according to our findings concerning the two species described here.