The isolates of Rhizopus collected from Korean traditional fermented food meju and nuruk, were compared with the well known species of Rhizopus donated. The isolates of Rhizopus were identified with the numerical analyses calculated from RAPD-DNA bands, and confirmed with the microscopic observations of morphological features on PDA. The isolates of R. oryzae purchased were segregated through the results of RAPD or the morphological features. The species of R. nigricans, known as an illegitimate species, were different from those of R. stolonife and it is estimated that they are species of Rhizopus, again. According to microscopic observations and the result of RAPD, Some isolates of R. oryzae purchased belong to R. nigricans and are completely different from R. oryzae in their growth. The isolates of R. nigricans included with several isolates of R. oryzae identified for the different phenotypes and were heterogenous. The isolate of R. oligosporus were speculated to be different from morphological features of Rhizopus, but to be similar to the species of Absidia on the apophysis of sporangium. Its sporangiophore or mycelium was observed to be dark black, but the sporangia were not in those of R. oligosporus. The isolates collected from Korean traditional nuruk showed genetic diversity, and also considered to be different tastes in Korean rice wines.