The carob moth, Ectomyelois ceratoniae Zeller (Lepidoptera: Pyralidae), is an insect pest that causes damage to various crops and fruit trees throughout the world. In Tunisia, this pest attacks date, pomegranate and citrus by seriously affecting the fruit quality. Therefore, the objective of this work is to investigate genetic variation in the carob moth among and within three host-plants by three RAPD markers. The results showed high genetic diversity in the pest. The mean percentage of polymorphic loci was 78.38 %. The total variance percentage of 5 % among populations and 95 % within the populations is suggestive of the role of sexual reproduction for generating high genetic diversity. The average genetic distances among populations ranged from 0.028 to 0.043. The date population is more related to the pomegranate population compared to citrus specimens. The UPGMA dendrogram and the two-dimensional principal component analysis (PCA) showed that there is no correlation between E. ceratoniae genotypes and their host plants and geographic localisation suggesting that gene flow between populations is independent of geographic distance and appears to be unrestricted.