Female meiosis and the rapid mitotic cycle of early embryos are two non-canonical cell cycles that occur sequentially in the same cell, the egg, and utilize the same pool of cell cycle proteins. Using a genetic approach to identify genes that are specifically required for these cell cycles in Drosophila, we found that a Drosophila Cks gene, Cks30A is required for spindle assembly and anaphase progression in both female meiosis and in the syncytial embryo. Cks30A interacts with Cdk1 to target cyclin A for destruction in the female germline, possibly through the activation of a novel germline specific CDC20 protein, Cortex. These results indicate that anaphase progression in female meiosis and the early embryo are under unique control in Drosophila.