The queenless ant, Pristomyrmex punctatus (F. Smith) reproduces parthenogenetically. The workers lay unfertilized eggs, which develop into female workers. This mode of reproduction generates hereditary clones. A previous research shows that when genetically monomorphic colonies were split, the workers tended to reassemble after being split into two groups, but when genetically polymorphic colonies split, they remained as two separate colonies. However, it remains unclear whether the workers can recognize individual genotype. Here, it was investigated whether individuals from geographically divergent, genetically monomorphic colonies would assemble with individuals of the same genotype. Two artificially fused colonies were prepared, A and B, comprising 200 individuals and 100 individuals, respectively. Each half of the artificially fused colony was composed of workers from two different genetically monomorphic source colonies. The workers assembled as a single colony when the genotype of the source colonies was identical. However, when the genotypes of source colonies were different, the workers did not assemble into one colony, but split into two groups according to genotype. These results suggest that P. punctatus can potentially recognize individual genotype, and select colony members based on an individual's genotype.