Plant development is regulated by external and internal factors such as light and chloroplast development. A revertant of the Arabidopsis thaliana chloroplast biogenesis mutant snowy cotyledon 3 (sco3) was isolated partially recovering the impaired chloroplast phenotype. The secondary mutation was identified in the Phytochrome B (PHYB) gene, involved in light mediated signalling, disrupting the PAS repeat domain required for light-induced nuclear localisation. An independent phyB mutation was crossed into sco3 mutants, resulting in the same partial reversion of sco3. Further analysis demonstrated that SCO3 and PHYB influence the greening process of seedlings and rosette leaves, embryogenesis, rosette formation and flowering. Interestingly, the functions of these proteins are interwoven in various ways, suggesting a complex genetic interaction. Whole-transcriptome profiling of sco3phyB indicated that a completely distinct set of genes was differentially regulated in the double mutant compared with the single sco3 or phyB mutants. Thus, we hypothesise that PHYB and SCO3 genetically suppress each other in plant and chloroplast development.