The physical organization of eight Tetrahymena genes active during conjugation (meiosis) was examined in the somatic (macro-) and germinal (micro-) nuclei of this organism. Three of these genes make transcripts that are only detected during meiotic prophase. Southern blot analyses indicated that all genes examined were present in both nuclei. Except for one gene family (pC6), all appeared to be non-repetitive and there were no detectable sequence rearrangements in or near the genes. The exceptional gene was repeated approximately five to seven times and DNA rearrangement occurred in or near each of these copies. A comparison of cDNA and macro- and micronuclear DNA restriction maps indicated that one of the genes (cnj B) contains introns. This is the first report of evidence for introns in a non-ribosomal gene in Tetrahymena. A site specific modification probably due to adenine methylation was seen in the macronuclear copy of another gene (cnj C).