Pecan, [Carya illinoinensis (Wangenh.) C. Koch], is a member of Juglandaceae family and is one of the most important nut crops produced in the United States. The objective of this study is to generate the first genetic linkage maps for pecan. Maps were constructed for the cultivars `Elliot' and `Pawnee' using the double pseudo-testcross mapping method whereby a separate linkage map is made for each parent using markers heterozygous in that parent. First generation maps consisted primarily of randomly amplified polymorphic DNA (RAPD) markers. We have now used fluorescently labeled amplified fragment length polymorphism (AFLP) markers to produce more complete maps. In the development of the AFLP markers, 64 primer combinations were originally screened to find the most informative combinations. Ten primer combinations were then chosen to produce markers for the maps. The maps currently consist of approximately 100 RAPD and 100 AFLP markers on each cultivar map. `Pawnee' is a high quality commercial pecan cultivar with a very early ripening date. `Elliot' possesses high levels of resistance to pecan scab, caused by the fungus Cladosporium caryigenum. The maps will be used to find markers linked to scab resistance genes and other traits of interest to the breeding program.