Subpopulation genetic structure was studied in a population of the short-lived perennial plant Alkanna orientalis from the Sinai Desert, Egypt. The population investigated was subdivided for sampling into four subpopulations, which were located within three steep-sided wadis and a central plain area. Results from previous studies suggested that bee pollinator behaviour was likely to cause limited gene dispersal within the population and that subpopulations might have diverged from each other genetically. Seven RAPD primers were used to detect polymorphisms in the population. Differences between sub-populations in fragment frequency were found for several of the 45 polymorphic RAPD fragments scored. Population subdivision was evident from cluster analysis, and an analysis of genetic distances showed that there was significant genetic differentiation between all subpopulations. Nevertheless, more extensive gene flow appears to take place within the population than was expected, as demonstrated by a higher level of genetic similarity between subpopulations from two of the narrow wadis and the interconnecting plain. It is suggested that seed transport mediated by periodic flash floods is responsible for this pattern.