The membrane‐associated mucin (MAM) domain containing glycosylphosphatidylinositol anchor 2 protein single knock‐out mice (MDGA2+/−) are models of ASD. We examined the behavioral phenotypes of male and female MDGA2+/− and wildtype mice on C57BL6/NJ and C57BL6/N backgrounds at 2 months of age and measured MDGA2, neuroligin 1 and neuroligin 2 levels at 7 months. Mice on the C57BL6/NJ background performed better than those on the C57BL6/N background in visual ability and in learning and memory performance in the Morris water maze and differed in measures of motor behavior and anxiety. Mice with the MDGA2+/− genotype differed from WT mice in motor, social and repetitive behavior and anxiety, but most of these effects involved interactions between MDGA2+/− genotype and background strain. The background strain also influenced MDGA2 levels and NLGN2 association in MDGA2+/− mice. Our findings emphasize the importance of the background strain used in studies of genetically modified mice.