The pairing and recombination of homologous chromosomes is crucial for their reductional segregation during meiosis I, but until now it has been unclear how chromosomes recognize their homologous partners. Ding et al. observed that fluorescently tagged sme2 loci, located on Schizosaccharomyces pombe chromosome 2, paired frequently in early meiotic prophase. When the sme2 locus was translocated to another region, robust pairing was seen at this ectopic site, indicating that sme2 is sufficient to induce robust homologous pairing. Furthermore, when two copies of sme2 were present on non-homologous chromosomes, the two loci associated transiently, suggesting that sme2 loci can recognize each other. Importantly, sme2 non-coding RNA transcripts, transcribed from both homologous chromosomes, accumulated at their respective gene loci and were found to be essential for pairing. Whether other pairing sites also exist on chromosome 2 remains to be determined.