Downregulation of protein phosphatase Cdc25 Twine activity is linked to remodelling of the cell cycle during the Drosophila maternal-to-zygotic transition (MZT). Here, we present a structure-function analysis of Cdc25 Twine . We use chimeras to show that the N-terminus regions of Cdc25 Twine and Cdc25 String control their differential degradation dynamics. Deletion of different regions of Cdc25 Twine reveals a putative domain involved in and required for its rapid degradation during the MZT. Notably, a very similar domain is present in Cdc25 String and deletion of the DNA replication checkpoint results in similar dynamics of degradation of both Cdc25 String and Cdc25 Twine . Finally, we show that Cdc25 Twine degradation is delayed in embryos lacking the left arm of chromosome III. Thus, we propose a model for the differential regulation of Cdc25 at the Drosophila MZT.