Research on educational assortative mating has devoted much attention to educational expansion but has been less focused on a concurrent trend of importance – growing differentiation among higher education institutions. This study proposes that the bifurcation between high- and low-tier institutions in the context of high participation in tertiary education may help us understand the mixed evidence on educational homogamy trends across countries. I focus on Japan, which is characterized by a clear and widely acknowledged hierarchy of institutional selectivity, as an interesting case study. By applying log-linear and log-multiplicative models to data from the Japanese Panel Survey of Consumers and the Keio Household Panel Study, I find the following results. First, the odds of homogamy are higher among graduates of selective (national/public) universities than among graduates of nonselective (private) universities. Second, homogamy trends among graduates of selective and nonselective universities have diverged in recent years. I discuss these diverging trends, which have been obscured in earlier studies, provide new insights into the role of educational assortative mating in the creation of stratification and inequality.