Sexual reproduction is a fundamental developmental process that allows for genetic diversity through the control of zygote formation, recombination, and gametogenesis. The correct regulation of these events is paramount. Sexual reproduction in filamentous fungi, including mating strategy (self-fertilization/homothallism or outcrossing/heterothallism), is determined by the expression of mating type genes at mat loci. Aspergillus nidulans matA encodes a critical regulator that is a fungal ortholog of the hSRY/SOX9 HMG box proteins. In contrast to well-studied outcrossing systems, the molecular basis of homothallism and role of mating type genes during a self-fertile sexual cycle remain largely unknown. In this study the genetic model organism, A. nidulans, has been used to investigate the regulation and molecular functions of the matA mating type gene in a homothallic system. Our data demonstrate that complex regulatory mechanisms underlie functional matA expression during self-fertilization and sexual reproduction in A. nidulans. matA expression is suppressed in vegetative hyphae and is progressively derepressed during the sexual cycle. Elevated levels of matA transcript are required for differentiation of fruiting bodies, karyogamy, meiosis, and efficient formation of meiotic progeny. matA expression is driven from both initiator (Inr) and novel promoter elements that are tightly developmentally regulated by position-dependent and position-independent mechanisms. Deletion of an upstream silencing element, matA SE, results in derepressed expression from wildtype (wt) promoter elements and activation of an additional promoter. These studies provide novel insights into the molecular basis of homothallism in fungi and genetic regulation of sexual reproduction in eukaryotes.S EXUAL reproduction is a central part of the life cycle in most eukaryotic organisms and has a profound impact on the evolution and biology of species. Successful exchange of genetic material requires establishment of sexual identity (male and female function). Sexual identity in animals is governed by genes located on sex chromosomes, whereas in fungi mating type genes residing at mat loci (sexual-identity loci) control cell-type identity and sexual development. The correct regulation and spatiotemporal expression of sex determining genes is crucial during reproduction. Mechanisms underlying gene regulation in eukaryotic sexual development are not well understood (Harley et al. 2003;Fraser and Heitman 2005;Kashimada and Koopman 2010). Mating type genes have been described in numerous heterothallic (cross-fertile) and homothallic (self-fertile) filamentous fungi, where they function as master regulators of sexual reproduction (Kronstad and Staben 1997;Debuchy et al. 2010). The mat loci typically encode transcription factors, either Mat-HMG (high-mobility group box) or Mat-a (alpha box), proteins that coordinate expression of sex-specific genes. Several lines of study indicate that mating type genes in fungi share structural and functiona...