Genetic populations used for linkage mapping are usually called mapping populations. The advent and development of molecular marker technology has generated renewed interest in linkage mapping in cotton since the mid-1990s. Genetic linkage mapping requires the creation of an appropriate mapping population and the development of markers for the mapping population. Mapping populations are usually developed from controlled crosses between two or more parents. Parent selection for developing a mapping population is critical to the success in constructing a linkage map for gene or quantitative trait locus (QTL) mapping in that parents must have sufficient phenotypic variation for the traits of interest and high genetic variation at the DNA sequence level. Consideration must be given to the source of parents (adapted or commercial vs. unadapted, exotic, or wild) within the same species, and even related species may be used as parents to make interspecific hybrid populations. Mapping populations can be divided into three types: (1) bi-parental populations, including F2, F2-derived F3 (F2.3), BC1F1, BC2F1, recombinant inbred lines (RILs), backcross inbred lines (BILs), chromosomal segment substitution lines, and near-isogenic lines (NILs); (2) multi-parent populations (MPPs), including nested association mapping (NAM) and multi-parent advanced generation intercross (MAGIC) populations; and (3) natural populations using existing germplasm accessions. This chapter deals with the development of different types of mapping populations and marker types used in cotton linkage mapping and genomic studies. The advantages and disadvantages of developing and using different populations and marker types are discussed. Relevant issues such as segregation ratios in different mapping populations and the size of mapping populations and number of markers are also discussed.