Identification of citrus genetic variability is prerequisite for effective genetic resources management and selection process in breeding program. The objective of the research was to study fifteen accessions of Indonesian functional citrus based on morphological characters and molecular marker. The research was conducted in Plant Breeding Laboratory, Indonesian Citrus and Subtropical Fruits Reserach Institute, Malang, West Java. The morphological variability was based on observation of morphological characters, while molecular variability was based on amplification of RAPD markers. Morphology and molecular diversities were analyzed by DARWin5 program. The results showed that morphological diversity is higher than molecular diversity. The highest morphology diversity occured between Citrumelo and Carrizo Citrange with seedless Lemon (79%), while the highest molecular diversity occured between Lemo Swangi with seedless Lemon (49%). The specific bands were found on Jari Budha, Etrog Citron, and seedless Lemon accessions using RAPD marker OPH15(235,280), on accession with trifoliate leaf (Troyer Citrange, Citrumelo, and Carrizo Citrange) using OPD07(400) and OPC17(416) and on Keprok Tening using OPH04(583) and OPD07(330).