Many morphological traits in cotton are qualitative in nature and controlled by one or two major genes with little or no environmental effects. Genetic studies of qualitative traits in cotton began with colored lint fibers, okra leaf, and red leaf right after the rediscovery of Mendelian Laws in 1900. Over 200 genes and alleles for different qualitative traits have been identified or transferred into tetraploid cotton through traditional Mendelian genetic studies using TM-1, T582, T586, and cytogenetic stocks. They are valuable sources for genetic and genomic studies, and many of them are useful in cotton breeding and production. Since the advent of molecular markers, linkage mapping to determine the chromosomal location of a mutant gene has become a common practice by crossing an existing or new cotton mutant with a normal cotton genotype including TM-1 or a commercial cotton cultivar. Thus far, more than 1/3 of known mutant genes and alleles are located to chromosomes, and more than 40 of them are mapped using molecular markers. Most importantly, more than 25 functional genes have been identified as underlying genes for many qualitative traits. This chapter will briefly review the progress in qualitative genetics and gene mapping and cloning in cotton, with a focus on plant color, height, type and trichome, leaf color and shape, flowers, glandless, fibers, and insect and disease resistance. Genome sequencing and bioinformatic tools have accelerated the progress in mapping and cloning qualitative trait genes. It is expected that many more functional genes will be identified for more morphological traits, especially those of agronomic importance.