Genetic variation in 12 populations of sea beet was assessed at nine isozyme and seven RFLP loci. Mean observed heterozygosity, diversity index and number of alleles per locus were not significantly different between the two classes of marker. The genetic structure of 10 of the populations was analysed using seven of the isozymes and six of the RFLPs. F-ST values between all pairs of populations were calculated separately for the isozymes and RFLPs. F-ST values were converted to amounts of gene flow (Nm) between populations under the assumptions of an island model. A regression of log Nm against log distance was used to test for isolation by distance. Mantel tests showed a highly significant decrease in Nm with distance for RFLPs but not for isozymes. It is suggested that uniform balancing selection may operate to maintain approximately equal allele frequencies among populations at the isozyme loci. If this is true then isozymes may be unsuitable for modelling the spread of neutral transgenes.