Autogamy is a sexual process of meiosis and self-fertilization which occurs in unpaired Paramecium cells and is considered to be coupled to the Paramecium clonal life span. In order to identify gene expression which may underlie the initiation of autogamy, we screened for genes differentially expressed before and after the onset of autogamy by using a subtraction strategy and obtained two species of difference genes. Both genes were found to be the ones increasingly expressed with clonal age that we have cloned previously. One was repressed upon commitment to autogamy and identified to be the α-51D surface protein gene. The other, progressively activated while paramecia traversed the autogamy pathway, was identical to the gene named MS2. Although we failed to structurally characterize the MS2 gene, it was suggested that continuous delivery to paramecia of double stranded RNA corresponding to a part of this gene impaired normal development of autogamy, implying direct involvement of MS2 in the process of autogamy.