Cordyceps species are important mushrooms traditionally used for heaths and vitality. C. sinensis has been widely used as a medicinal mushroom and C. militaris is popular for its substitute. C. militaris can be cultivated artificially and new strains has been improved by crossing single spore strains. As a bipolar heterothallic fungus C. militaris has two strains of compatible mating types and they can be differentiated by crossing, fruiting body formation ability and the production of perithecia. However this process is very laborious and time consuming to carry out. In this study, molecular markers were designed and used for the detection of two opposite mating types. Two mating types were assayed using two sets of primers specific for C. militaris, which were amplified a 191-bp fragment for MAT1-2 and 233-bp fragment for MAT1-1. After crossing of two compatible mating types F1 hybrids resulted in well-developed perithecial fruiting bodies and their crossings were confirmed by the multiplex PCR assays for the rapid and specific detection of both MAT1-1 and MAT1-2. This results may serve as a efficient process in the breeding program for artificial cultivation and industrial-scale production of C. militaris.