The species of genus Capsicum are synthesizing capsaicinoids – alkaloids that give pungency in peppers. The most pungent capsaicinoids are capsaicin and dihydrocapsaicin. Capsaicin is the component of chili peppers which is irritant for mammals, including humans, and produces a sensation of burning in any tissue with which it comes into contact. Pungency as a feature has two aspects – quantitative and qualitative – affected by the way the general biosynthetic pathway of capsaicin and other capsaicinoids’ synthesis is affected. Capsaicin is synthesized in the interlocular septum of plants of the Capsicum genus and its production is qualitatively controlled by the Pun1 locus. It was found that the locus contains a putative acyltransferase. Several mutant alleles of Pun1 gene were identified through classical breeding methods as responsible for the loss of pungency. Furthermore, the mutation in another locus (Pun2) was also found to affect the levels of capsaicin production thus providing evidence for the presence of a second gene with a major epistatic effect on capsaicin production. Here we review the current state of the knowledge accumulated so far as regards the alleles and their interactions that affect the production of this compound. The less pronounced effects of other genes in the biosynthetic pathway and some transcription factors are also discussed.