In Afghanistan, pistachio (Pistacia vera L.) is found mainly in the wild in natural forests. In this study, 17 wild Afghan pistachio accessions and three cultivated genotypes were characterised using amplified fragment length polymorphisms (AFLPs). Material was sampled mainly from the Kunduz and Takhar regions. A total of 288 AFLP fragments were generated using eight AFLP primer combinations. The number of amplified fragments varied from 18 - 48 per primer combination, and 136 bands were polymorphic, with an average of 17 polymorphic bands per primer combination. The percentages of polymorphic bands ranged from 26.2 - 79.2 per primer pair. According to UPGMA clustering of the Nei and Li distance matrix, the 17 wild accessions were grouped according to their region of origin and were distinct from the three cultivars. The AFLP technique was found to be effective for characterising wild P vera material, which was genetically the closest to cultivated pistachio.