The maternal effect locus fs(1) Ya is required for the fusion of the apposed sperm and egg pronuclei (syngamy) following fertilization in Drosophila. It is tightly linked to another complementation group, fs(1) Yb, needed for both oogenesis and embryogenesis. We have isolated a set of overlapping cloned sequences in the 3B4-6 region of the X chromosome encompassing the fs(1) Ya-fs(1) Yb region. A single 2.4 kb maternal transcript is encoded within this region, and an 8.5 kb DNA fragment that contains this transcript complements both fs(1) Ya and fs(1) Yb mutations. Northern and in situ hybridization analyses show that the maternal transcript is only present in nurse cells and oocytes beginning in previtellogenic stages, and is evenly distributed in the cytoplasm of 0-2 h syncytial embryos. The transcript is not detected in later stages of embryonic development. This expression pattern correlates closely with the genetic and developmental characteristics expected of the fs(1) Ya gene product.