Early blight (EB), caused by the fungus Alternaria solani, is a destructive disease of tomato (Lycopersicon esculentum) worldwide. Sources of genetic resistance have been identified within related wild species, including green-fruited L. hirsutum and red-fruited L. pimpinellifolium. We have employed traditional protocols of plant breeding and contemporary molecular markers technology to discern the genetic basis of EB resistance and develop tomatoes with improved resistance. Backcross breeding has resulted in the development of germplasm with improved resistance; however, linkage drag has been a major obstacle when using L. hirsutum as a donor parent. To identify and map QTLs for EB resistance, we used several filial and backcross populations derived from interspecific crosses between L. esculentum and either L. hirsutum or L. pimpinellifolium. In each population, an average of seven resistance QTLs were detected. While similar QTLs were detected in different generations of the same cross, generally different QTLs were identified in populations derived from different crosses. The results suggested stability of QTLs across environments and generations but variation in QTLs in different interspecific populations. It is expected that marker-assisted pyramiding of QTLs from different sources results in development of germplasm with strong and durable resistance. Further inspection of the results led to the identification and selection of six QTLs with stable and independent effects for use in marker–assisted selection (MAS). However, to facilitate “clean” transfer and pyramiding of these QTLs, near-isogenic lines (NILs) containing individual QTLs in a L. esculentum background should be developed.