Hydrogen production rates by photosynthetic organisms are relatively low, and methodologies traditionally used to enhance those rates typically achieve moderate improvements of natural rates. This limitation is in part due to the absence of methods for high-throughput screening of hydrogen production by biological systems. This work focuses on methodology for non-designed enhancement of hydrogen production activity through the detection of rare overproducers within a very large population of cells. We build on a previously generated high-throughput screening tool and select hydrogen overproducing strains generated by genome-wide random mutagenesis of Rhodobacter capsulatus. Selected strains produce up to 3-fold more hydrogen than the parental strain in batch cultures, and up to 19-fold more when cultured in a chemostat. One outcome from this work is that this method did not accumulate mutations on nitrogenase or hydrogenase genes, which would be obvious targets for a designed mutant strategy. It appears that a panoply of mutations, probably resulting in small production increments, underly the hydrogen overproducing phenotype.