A group of 22 Citrus varieties (sweet oranges, lemons, grapefruits, clementines and several other mandarin biotypes) was analysed by isozyme and RAPD markers in order to assess their genetic relationships. Four isozyme systems (GOT, IDH, PGM and PGI) revealed seven loci, four of them polymorphic. Sweet oranges, lemons, grapefruits and clementines were discriminated at the species level but individual varieties within each species remained undistinguishable by the analysed isozyme systems. Nevertheless, a specific isozyme pattern was found for almost each one of the mandarin varieties with the exception of Carvalhais and Fremont, which shared an identical isozyme pattern. Additionally, RAPD analysis was carried out using 36 decamer primers that revealed 289 markers, 48.4% of which were polymorphic. The RAPD technique. though discriminating among all the species and distinguishing among the mandarin varieties, including Carvalhais and Fremont, was unable to discriminate among the different varieties within the remaining Citrus species (biotypes).