In Neurospora crassa, mating and heterokaryon formation between opposite mating-types is controlled by a single locus with two alternate forms termed mt A and mt a. Previously, an open reading frame (mt A-1) that confers mating identity and heterokaryon incompatibility was characterized in the 5.3 kb mt A idiomorph. In this study, we describe the structural and transcriptional characterization of two additional genes in the mt A idiomorph, Mt A-2 and mt A-3. The 373 amino acid mt A-2 ORF has 23% identity to the SMR1 ORF of Podospora anserina. DNA sequence analysis of a mutation affecting ascospore to 129 amino acids. The 324 amino acids mt A-3 ORF has an HMG domain and shows 22% amino acid identity to SMR2 of P. anserina. Transcripts from mt A-2 and mt A-3 are constitutively expressed during both vegetative and sexual reproduction. The presence of upstream ORFs in the mt A-2 and mt A-3 transcripts suggests the possibility of post-transcriptional regulation of the expression mt A-2 and mt A-3 polypeptides.