Simple sequence repeats (SSR) or microsatellites (MS) can develop to valuable markers for plant breeding because the SSR have several advantage features such as co-dominant, multiallelic loci and high polymorphism allowing precise discrimination even these mapping were closely related to individuals. Detection of variation by SNP (Single Nucleotide Polymorphisms) marker is used mainly in bacteria virus and human beings, but in plants their applications is very limited and still the use of genetic linkage maps and QTL (Quantitative Trait Loci) analyses is most efficient way to develop molecular markers. In this study, we have been constructing two genetic linkage maps for pepper using the SSR markers and F2 populations derived from interspecific population for FP11 (C. annuum) cross FP13 (C. chinense) and intraspecific population FP12 (C. annuum) cross FP16 (C. annuum) respectively. In the interspecific population, a total of 190 F2 individuals were subjected to construction of the genetic linkage map mounted on 2,328 markers. The SSR markers were consisting markers come from BAC end sequencing (BES), EST sequences and public sources, respectively. In the intraspecific population, a total of 190 F2 individuals were subjected to construction of the genetic linkage map mounted on 605 markers too. We were used together 2,933 markers construct an integrated map with MapDisto 1.7b and drawn using the MapChart 2.2 program. This interspecific map [FnP(AC)] was consisted 12 linkage groups covered 6,651 centimorgans (cM) on the LOD 6 with average interval distance of 2.9 cM. The intraspecific map [FnP(AA)] was consisted 14 linkage groups covered 3,001 cM on the same LOD score with average interval distance of 5.0 cM. The high density integrated pepper map constructed will be use to Marker-Assisted breeding and genetic reference for Capsicum species.