The Rhizopus strains in the Universitas Indonesia Culture Collection (UICC) were isolated from tempeh from various regions in Indonesia. Previous identification using phenotypic-based characters (morphology and physiology) has identified five strains of Rhizopus (UICC 27, UICC 40, UICC 51, UICC 67, and UICC 116) as R. oligosporus. The aim of this study was to re-identified five Rhizopus strains based on internal transcribed spacer (ITS) regions of ribosomal DNA sequence data. The phylogenetic tree was constructed by neighbor-joining method with Kimura's two parameters model. The basic local alignment search tool (BLAST) sequence homology search showed that all strains have low homology (91%) to the type strain of R. oligosporus (syn. of R. microsporus CBS 357.93T). However, they have high homology (99%) to R. oryzae CBS 112.07T type strain. The phylogenetic tree showed that these five strains were distantly related to the group of R. microsporus CBS 357.93T type strain. The UICC 116 strain was included in a monophyletic group with R. oryzae CBS 112.07T type strain, while the other four strains (UICC 27, UICC 40, UICC 51, and UICC 67) were included in a monophyletic group with R. delemar CBS 120.12T type strain. The phylogenetic tree showed that the R. delemar group was phylogenetically very closely related with R. oryzae group. In this study, four Rhizopus strains (UICC 27, UICC 40, UICC 51, and UICC 67) were identified as R. delemar, while UICC 116 strain was identified as R. oryzae. Morphological characterization indicated that all strains showed morphological characters which corresponded to R. oryzae.