This study was performed to construct the first genetic linkage map of pistachio using progeny from a cross between Pistacia vera L. 'Siirt' and monoecious Pistacia atlantica Desf. (Pa-18 genotype). In total, 242 primers were screened. Seventy inter-simple sequence repeat (ISSR), sequence-related amplified polymorphism (SRAP), and amplified fragment length polymorphism (AFLP) primer pairs were chosen, and they produced 321 segregating markers. A double pseudo-testcross mapping strategy was applied to construct the 'Siirt' and 'Pa-18' maps. The 'Siirt' map consisted of 144 testcross and 21 intercross markers, and the 'Pa-18' map included 134 testcross and 22 intercross markers. The 'Siirt' map had 17 linkage groups spanning 1237.3 cM with a mean marker density of 7.50 cM, while the 'Pa-18' map comprised 19 linkage groups covering 1337.5 cM, with the average marker density being 8.57 cM. One hundred fifty-seven of the segregating markers were distorted, of which 38.2% were in the 'Siirt' map, and 60.3% were in the 'Pa-18' map. The maps of P. vera and monoecious P. atlantica may help to clarify the genetic basis of sex determination and inheritance in Pistacia, as well as other notable agronomic characters, and in identifying markers for marker-assisted selection. (C) 2012 Elsevier B.V. All rights reserved.