In metazoan germ cells, transposable element activity is repressed by small noncoding PIWI-associated RNAs (piRNAs). Numerous investigations in Drosophila have enlightened the mechanism of this repression in the adult germline. However, very little is known about piRNA-mediated repression during germline development. Nevertheless, to maintain the integrity of the genome, repression should occur throughout lifespan of germ cells. Here, we show that piRNA-mediated repression is active in the female germline from late embryonic to pupal primordial germ cells, and that genes related to the adult piRNA pathway are required for repression during development. rhino-dependent piRNAs exhibiting the molecular signature of the piRNA pathway "ping-pong" amplification step are detected in larval gonads. Furthermore, as in adult ovaries, we can observe an incomplete, bimodal and stochastic repression resembling variegation at all developmental stages. We strongly suggest, using clonal analyses, that this variegation reflects a cellular memory of an early repression decision taken in embryonic germ cells. This study shows that piRNAs and their associated proteins are the epigenetic components of a continuous repression system throughout germ cell development.