Random amplified polymorphic DNA polymerase chain reaction (RAPD–PCR) was used to assess the genetic diversity in twelve populations (a total of 144 isolates) of the Pleurotus eryngii complex, sampled in Israel. Our results show a higher level of diversity of RAPD polymorphism in the populations, especially in the drier, stressful climates. Twelve primers used in this study amplified 164 scorable RAPD loci, of which 163 (99.4%) were polymorphic and only 1 monomorphic. Out of the 164 loci, 123 (75%) varied significantly (P < 0.05) in allele frequencies among populations. This total proportion (75%) of significant polymorphic loci far exceeds the 5% level expected by chance (binomial test, P < 0.000001). The levels of polymorphism and gene diversity appeared to be highly significantly different between the populations. Sixty-eight per cent of the RAPD diversity was within populations and 32% was between populations. Inter-population genetic distances showed positive association with geographic distance, which was confirmed with spatial autocorrelation analysis of RAPD frequencies. Spearman rank correlation revealed a strong positive association between high polymorphism and the aridity index. In multiple regression, the coefficient of determination of polymorphism and gene diversity was explained by climatic variables linked to temperature and humidity. Our findings further demonstrate the validity of the ‘environmental theory of genetic diversity' hypothesis within P. eryngii populations in Israel. We suggest that natural selection develops a high level of RAPD polymorphism as adaptation to cope with stressful and temporally heterogeneous environments.