Maize (Zea mays L.) breeders commonly assign inbred lines to groups in order to maintain the high level of hybrid vigor obtainable from crosses. It had already been reported that the genetic similarity estimated from 60 SSR loci was effective for the assignment of maize inbred lines derived from European hybrids, which contain mixtures of dent and flint germplasm, to dent or flint groups adapted to the cold regions of Japan. We evaluated a simplified assignment method using a smaller number of SSR loci. Two subsets were chosen from the full set of 60 SSR loci distributed uniformly throughout the maize genome. Set 1 composed of 25 loci and Set 2 composed of 14 loci were chosen based on the difference in allele frequency (0.4 for Set 1 and 0.5 for Set 2) between dent and flint groups. SSR loci of Set 1 and Set 2 carried a total of 176 and 99 alleles among 88 inbred lines, respectively. The numbers of alleles for Set 1 and Set 2 were 38% and 21% of the number of alleles for the full set of SSR loci, respectively. The assignments based on mean genetic similarity estimates using Set 1 SSR loci almost all corresponded to those using the full set of SSR loci. Furthermore, the assignments of several inbred lines based on Set 1 SSR loci were ascertained by testcross data. The results indicated that the assignment using Set 1 SSR loci with a similar accuracy to that of the full set of SSR loci is an efficient method in a maize breeding system.