Pepper is an important commercial crop because of its unique pungency. Pepper is also widely used as a research material. Until recently, most genomic studies on pepper were carried out using genetic maps. The chromosome numbering of pepper was carried out by comparing the genetic maps of pepper and tomato. Comparative analysis of the genetic maps of pepper and tomato revealed recombinations, inversions and translocations in the pepper genome. The construction of bacterial artifi cial chromosome (BAC) libraries enabled comparative analyses of pepper and other Solanaceous species at a fi ner level. The pepper whole genome sequencing project was recently launched and is making progress. This chapter summarizes the prior research on pepper genome and describes the pepper genome sequencing project that is currently in progress.