Summary: The Polycomb Group proteins are required for stable long‐term maintenance of transcriptionally repressed states. Two distinct Polycomb Group complexes have been identified, a 2‐MDa PRC1 complex and a 600‐kDa complex containing the ESC and E(Z) proteins together with the histone deacetylase RPD3 and the histone‐binding protein p55. We report here that there are at least two embryonic ESC/E(Z) complexes that undergo dynamic changes during development and a third larval E(Z) complex that forms after disappearance of ESC. We have identified a larger embryonic ESC complex containing RPD3 and p55, along with E(Z), that is present only until mid‐embryogenesis, while the previously identified 600‐kDa ESC/E(Z) complex persists until the end of embryogenesis. Constitutive overexpression of ESC does not promote abnormal persistence of the larger or smaller embryonic complexes and does not delay a dissociation of E(Z) from the smaller ESC complex or delay appearance of the larval E(Z) complex, indicating that these changes are developmentally programmed and not regulated by the temporal profile of ESC itself. Genetic removal of ESC prevents appearance of E(Z) in the smaller embryonic complex, but does not appear to affect formation of the large embryonic ESC complex or the PRC1 complex. We also show that the ESC complex is already bound to chromosomes in preblastoderm embryos and present genetic evidence that ESC is required during this very early period. genesis 35:114–124, 2003. © 2003 Wiley‐Liss, Inc.