The genus Gossypium has small, pigmented glands filled with a terpenoid aldehyde, gossypol, in many parts of the plant including the seed. Gossypol limits food utilization of cotton seed due to its toxicity to human and non-ruminant animals. Because the genesis of gossypol is closely related to gland morphogenesis, we report the results on the identification of functional markers for gland morphogenesis in cotton. A total of eighty-five unique, gland development-related protein (GDRP) mRNA sequences were collected from NCBI GenBank. Intron-flanking regions within GDRP genes were amplified using 156 primers designed from exon/exon junction sites inferred from Arabidopsis homologous sequences. Intron size polymorphism was not detected in this study between G. hirsutum cv. TM-1 and G. barbadense cv. 3-79. Therefore, 30 purposely selected GDRP PCR products were subsequently sequenced to identify single nucleotide polymorphisms (SNPs). A total of forty SNPs including six indels were identified in 16,328 nucleotides of GDRP coding and intron sequences. We genotyped all SNP markers against 188 recombinant inbred lines (RILs) previously developed from a cross between TM-1 and 3-79 and located 36 SNP markers (24 loci) to the cotton genome. The 24 loci mapped in this study were distributed among the 15 chromosomes of allotetraploid cotton. Localization of functional genes in the cotton genome would facilitate the discovery of candidate genes associated with gland/gossypol traits and would increase the utility of previously developed genetic markers for cotton seed improvement.