Tomato mottle virus (ToMoV) is a whitefly transmitted geminivirus threatening the Florida fresh-market tomato (Lycopersicon esculentum Mill.) industry. ToMoV resistance was identified in Lycopersicon chilense accessions LA 1932, LA 1938, LA 1969, and LA 2779, and introgressed into tomato breeding lines. Inheritance studies of populations derived from resistant accessions of LA 1932 and LA 1938 suggest that introgressed resistance is largely additive and multigenic. RAPD polymorphisms were identified using 800 arbitrary primers (decamers), and 88 polymorphisms with good repeatability were identified. Of these, 45 polymorphisms were identified in breeding lines derived from two or more of the four accessions. Analysis of segregating F2 populations has resulted in association of RAPD markers with geminivirus resistance genes, and markers have been identified that are common to different L. chilense resistance sources. Linkage of several markers to each other and to the self pruning (sp) and β-carotene (B) loci on chromosome 6 was also determined.