Random amplified polymorphic DNA (RAPD) analysis and multilocus enzyme electrophoresis (MLEE) were used to assess genetic variability in six wild populations and in five laboratory strains of Ceratitis capitata. The RAPD technique reveals larger amounts of genetic variation than the conventional MLEE, and can improve discrimination within and between populations and strains. In our experimental conditions, RAPD analysis with four different primers produces 174 polymorphic bands out of 176, while MLEE analysis at 26 enzyme loci scores 74 alleles. RAPD fingerprints are peculiar to African flies, while different laboratory strains have similar patterns, independently of their origins. The results obtained by these two methods are significantly correlated, and are in agreement with the general trend of decreasing variability from African populations towards the peripheral and laboratory ones. UPGMA dendrograms derived from MLEE (protein) and RAPD (DNA) data show that a major part of intraspecific variability involves the differentiation of central vs. peripheral populations.