Replication of the eukaryotic genome requires the assembly of thousands of replisomes that must work in concert to accurately replicate a cell’s genetic and epigenetic information. Defining replisome-associated proteins is a key step in understanding how genomes are replicated and repaired in the context of chromatin to maintain genome stability. To identify replisome-associated proteins, we performed iPOND (Isolation of Proteins on Nascent DNA) coupled to quantitative mass spectrometry in Drosophila embryos and cultured cells. We identified 76 and 416 replisome-associated proteins in post-MZT embryos and Drosophila cultured S2 cells, respectively . By performing a targeted screen of a subset of these proteins, we demonstrate that BRWD3, a targeting specificity factor for the DDB1/Cul4 ubiquitin ligase complex (CRL4), functions at the replisome to promote replication fork progression and maintain genome stability. Altogether, our work provides a valuable resource for those interested in the DNA replication, repair and chromatin assembly during development.