The mesotelencephalic dopamine system is genetically variable and affects motor behavior, motivation, and learning. Here we examine the genetic variation of mesencephalic DA neuron number in a quasi-congenic RQI mouse strain and its background partner and in a recombinant inbred strain with different levels of mesencephalic tyrosine hydroxylase activity (TH/MES). We used B6.Cb4i5-alpha6/Vad, C57BL/6By, and CXBI, which are known to express high, intermediate, and low levels of TH/MES, respectively. Unbiased stereological sampling with optical disector counting methods were employed to estimate the number of TH-positive neurons in the A8-A9-A10 cell groups. Morphometric studies on the mesencephalic dopamine cell groups indicated that male mice of the B6.Cb4i5-alpha6/Vad strain were endowed with a significantly lower number of TH-positive cells than CXBI mice. In all strains studied, the right retrorubral field (A8 area) had a higher number of dopamine neurons compared to the left A8 area. The results suggest an inverse relationship between TH/MES and number of dopamine neurons in the A9-A10 cell groups and significant lateral asymmetry in the A8 cell group. A detailed anatomical atlas of the mesencephalic A8-A9-A10 dopaminergic cell groups in the mouse is also presented to facilitate the assignment of TH-positive neurons to specific cell groups.