To overcome efficiency losses due to overheating in outdoor photobioreactors for microbial hydrogen production, heat-resistant microorganisms are desirable. In this study, the comparative whole genome sequencing analyses of two previously obtained Rhodobacter capsulatus heat-resistant mutants; A52 and B41, with modified hydrogen production capacities, have been performed to identify mutations related to hydrogen production. In comparison with the reference strain DSM1710, the genomes of the mutants A52 and B41 contained 2137 and 2253 mutations, respectively. In the mutant B41 genome, mutations were characterized within the nifD, nifj, gInD, nifB1, ccpA, hupD, dmsA, and cbbR1 genes. On the other hand; in the A52 mutant, mutations were characterized in the nifB2, rnfF, nifj, cbbO, anfH, amt, moeA, and hupD genes. The effects of nitrogen metabolism and redox-related mutations were tested by quantitative reverse transcription PCR. The most promising mutation was found on the gInD gene of B41 strain with higher hydrogen production capacity. (C) 2017 Hydrogen Energy Publications LLC. Published by Elsevier Ltd. All rights reserved.