A genetic linkage map of the sweet pepper (Capsicum annuum L.) using an intraspecific doubled-haploid (DH) population was primarily constructed by amplified fragment-length polymorphism (AFLP) using the high efficiency genome scanning (HEGS) system and random amplified polymorphic DNA (RAPD). Linkage analysis was done using a total of 518 molecular markers that consisted of 382 AFLP, 122 RAPD, 3 RFLP, 7 SCAR and 4 CAPS markers. The linkage groups consisted of 11 large linkage groups (56.7 to 118.5 cM) and 5 small linkage groups (1.8 to 33.1 cM), covering a total distance of 1043.1 cM with an average distance between 224 framework markers of 4.6 cM. AFLP markers could be developed quickly using HEGS, even in an intraspecific DH population in which it is generally difficult to detect polymorphisms in comparison with interspecific crossing populations. The map was constructed essentially in two months. Linkage analysis also provided three AFLP markers and an RAPD marker linked to PMMoV resistance (L³), and an AFLP marker linked to C that was required for expression of pungency. A closer marker linked to C, Plastid-lipid-Associated Protein-simple sequence repeat (PAP-SSR), a microsatellite marker linked to C, was found at a distance of 0.6 cM. We examined the usefulness of PAP-SSR with three species in Capsicum using fragment analysis and nucleotide sequences, many alleles were found at this locus. The results suggested that these markers could be effective in marker-assisted selection (MAS) programs for sweet pepper breeding purposes.