Vollenhovia emeryi ant is distinguished by its wing morphology; short winged (SW) and long winged (LW). Its reproduction shows a bizarre genetic caste system distinct from other social hymenopteran insects. Unfertilized eggs undergo genome duplication and develop into clonal gynes. Fertilized eggs develop either into workers or males. The fate of the fertilized eggs is determined whether maternal genome loss (MGL) takes place after fertilization. Eggs with MGL become haploid males with only paternal half of the genome. Without MGL, the eggs become workers with maternal and paternal half of the genome. In this research, we analysed 5 nuclear genes of SW and LW individual ants. Among them, two genes from an SW male are identical to those of LW, and one gene from the SW male seems a variant of LW. The result indicates that SW males are derived from LW colonies. From the genetic relatedness point of view individuals in the same castes are genetically identical. On the other hand, between workers and two reproductives, the relatedness is asymmetrical and there is even no gene sharing between gynes and males. The conventional genetic relatedness by Hamilton is revised under this condition.