Microsatellite primers were developed from bacterial artificial chromosome (BAC) end sequences (BES) of Citrus clementina and their transferability and polymorphism tested in the genus Citrus for future anchorage of physical and genetic maps and comparative interspecific genetic mapping. Using PAGE and DNA silver staining, 79 primer pairs were selected for their transferability and polymorphism among 526 microsatellites mined in BES. A preliminary diversity study in Citrus was conducted with 18 of them, in C. reticulata , C. maxima , C. medica , C. sinensis , C. aurantium , C. paradisi , C. lemon , C. aurantifolia, and some papedas (wild citrus), using a capillary electrophoresis fragment analyzer. Intra and interspecific polymorphism was observed, and heterozygous markers were identified for the different genotypes to be used for genetic mapping. These results indicate the utility of the developed primers for comparative mapping studies and the integration of physical and genetic maps.