Cell division is an essential cellular process that requires an array of known and unknown proteins for its spatial and temporal regulation. We developed a novel, highly sensitive, high-throughput screening method for the identification of bacterial cell division genes and regulators. The method combines the over-expression of shotgun genomic expression libraries to perturb the cell division process, with high-throughput flow cytometry sorting to screen many thousands of clones. Using this approach, we recovered clones with a filamentous morphology from two model bacteria, Escherichia coli and Bacillus subtilis. Genetic analysis revealed that our screen identified both known cell division genes, and novel candidate filamentation genes. This novel screening strategy is applicable to a wide range of organisms, including pathogenic bacteria, where cell division genes and regulators are attractive drug targets for antibiotic development.