Cultivated species of pepper (Capsicum sp.) are grown worldwide primarily for their flavor and high quality source of vitamins and antioxidants. Pepper is amenable to classical and molecular-genetic analyses and genomic resources are becoming increasingly available in pepper and other related genera in the Solanaceae family. In addition, selfing and crosses among and within the 5 cultivated species can be readily made and multiple generations can be produced each year. Over the past 20 years, a variety of molecular markers have been developed and applied to several intra- and inter-specific crosses including EST databases representing about 31,000 unigenes. Although integrated maps of approximately 2,200 anonymous markers exist, only 250 of these are known to represent genes. Taking advantage of genetic replication and Affymetrix GeneChip® technology, we have been able to use parallel high-throughput marker discovery to identified high quality markers for genetic mapping of inter- and intra-specific pepper RIL populations. In total, we were able to genetically map markers representing 16,188 and 3,892 unigenes (assembled ESTs) from C. frutescens x C. annuum and C. annuum x C. annuum populations respectively. A comparison of 2,622 unigenes common to both maps revealed high co-linearity with one large translocation and several regions of potential genomic rearrangement likely between C. frutescens and C. annuum. The implication of these maps in genomics, gene discovery and plant breeding of pepper will be discussed.