Some Asian black bears inhabiting Japan are known to invade residential areas, a phenomenon known as mass intrusion. Although mass intrusion occurs in autumn, it can result in genetic mingling. We examined the influence of intrusion on the genetic structure of black bears. Tissue samples were collected from invasive bears in central Japan in the autumn of two mass-intrusion years, 2004 and 2006. We also set hair traps overlapping an area where tissue samples were collected in the summers of 2005, 2006, and 2008. The genotypes of eight microsatellite loci were determined by PCR. Pairwise relatedness (r_xy) was negatively correlated with distance among resident bears, whereas no such relationship was observed among invasive bears. Spatial autocorrelation analysis of the normal bears in 2006 revealed a significantly positive rc value within the 0–65-km-distance class, whereas that of invasive bears in 2006 revealed significantly positive rc values between the 0–15- and 0–65-km-distance classes. We therefore concluded that mass intrusion enabled genetic mingling in autumn leading to alteration of the genetic structure; however, the normal structure subsequently recovered with seasonal movement.