Diversity and genetic relationships were investigated in 19 trifoliata oranges [(Poncirus trifoliata (L.) Raf] and their 27 hybrids including 20 citranges (P. trifoliata X Citrus sinensis), five citrumelos (P. trifoliata X C. paradisi) and two citremons (P. trifoliata X C. limon) based on inter-simple sequence repeat (ISSR) markers. Twelve ISSR primers produced a total of 120 fragments and 82 of them were polymorphic (68%). The unweighted pair group method arithmetic average (UPGMA) analysis as assessed with ISSR data demonstrated that the accessions had a similarity range from 0.67 to 1.00. In the dendrogram there were three main groups including trifoliata. citremon and citrange-citrumelo groups. The trifoliata orange, citrange, citrumelo and citremon groups were separated The citrumelo group was nested in the citrange branch. Genetic diversity among the trifoliata accessions was low probably because of their mutation origin. However all trifoliata accessions were distinguished except for two of them. The citrange group had higher polymorphism than the other trifoliata hybrids. Our study indicated that ISSR markers were usefull to determine genetic diversity of related citrus groups such as trifoliata oranges and their intergeneric hybrids.