Insects are the most diverse organisms in the world and have been in existence since ca. 480 Ma; given this, they can provide profound insights into evolution. Among them, the order Ephemeroptera is one of the most basal clades of winged insects. This makes Ephemeroptera a significant key taxon in understanding the macro-evolution or the insect groundplan. In the development of biological evolutionary studies of this taxon, it is important to establish a technique for cross-breeding. Furthermore, the establishment of these techniques also makes a great contribution in the fields of micro-evolution. In a non-model taxon, the mayfly, subcultivation in the laboratory has been thus far considered impossible. With the exception of some parthenogenetic strains, it is extremely difficult to mate these insects in artificial environments. In this study, we established a successful artificial mating technique, i.e., a “hand-pairing” based cross-breeding method for mayflies. Furthermore, we also succeeded in clearly verifying by a genotyping method that the offspring reproduced by hand-pairing were in fact derived from the actual male and female which were used for hand-pairing. We established a reproductive experimental technique for hand-pairing of Dipteromimus tipuliformis and verified this technique by means genotyping. This technique could allow the artificial control of fertilization timing, and result in offspring which can be verified as to their status by means of genotyping. This achievement will be extremely important in the future for both the macro- and micro-evolutionary studies of insects.