Overlapping genes that are transcribed from the same genomic regions are rare in eukaryotes and to date few detailed functional analyses have been reported. We report here three novel overlapping transcripts that are specifically expressed during meiosis of Schizosaccharomyces pombe. They are denoted as omt1+, omt2+ and omt3+ after overlapping meiotic transcripts. omt1+ encodes a 12-kDa protein and omt2+ encodes a 11-kDa protein with homology to the bifunctional mammalian protein DCoH/PCBD. omt3+ does not have a significant open reading frame. The omt2+ transcript overlaps with both the omt1+ and omt3+ transcripts but the latter two transcripts do not overlap. omt1Delta and omt2Delta but not omt3Delta failed to form mature spore walls. The Omt1-GFP and Omt2-GFP fusion proteins localized to the outside and the inside of the spore walls, respectively. The sporulation-specific protein Meu10 and the spore wall components were abnormally localized in the spore walls of omt1Delta and omt2Delta. The overlapping genes omt1+ and omt2+ express functional proteins that participate in spore wall maturation, indicating that gene overlap does not affect the physiological functions of the proteins encoded by these genes. Generation of overlapped RNA may be due to loose regulation of transcription termination during meiosis of S. pombe.