Dioecy in the model dioecious plant Silene latifolia is determined genetically by its heteromorphic sex chromosomes. A bacterial artificial chromosome (BAC) clone, #19B12, was isolated by screening a BAC library from S. latifolia using polymerase chain reaction (PCR) with a set of sequence tagged site (STS) primers, ScD05, which are specific to the Y chromosome. A portion of #19B12 was subcloned to construct plasmid #25-1, with an insert of 7.8 kb. This 7.8-kb fragment encodes ScD05 homolog and an anther-specific gene, CCLS96.1. Northern blot analysis of CCLS96.1 indicated a faint band of 1.8 kb in male and female flower buds. 5' and 3' rapid amplification of cDNA ends (RACE) indicated that transcripts of CCLS96.1 are very varied in size. Moreover, semi-quantitative reverse transcription-PCR (RT-PCR) showed that CCLS96.1 was also expressed in both male and female leaves. RACE produced at least ten species of transcripts, with 79-97% similarity among them. However, no significant ORFs could be predicted from their nucleotide sequences, since each has numerous stop codons throughout all three reading frames. Genomic Southern hybridization showed that the S. latifolia genome contains numerous CCLS96.1 homologs. These results suggest that the transcripts of CCLS96.1 play some role as multiple non-coding RNAs in S. latifolia.