The effect of four mutated genes affecting anthocyanin biosynthesis was investigated relative to tomato and pepper germination capacities and early seedlings and plantlets growth. The study was performed on isogenic/near isogenic lines (IL/NIL) differing for genes ah (Hoffmann’s anthocyaninless), aw (anthocyanin without) and bls (babylea syndrome) in tomato and al ₁ (anthocyaninless – 1) in pepper. Germination responses of the IL/NILs showed that genes ah, aw and bls in tomato and al ₁ in pepper enhanced germination abilities under stress conditions regardless of the inherent seed properties that imparted rapid germination. This evaluation was conducted with four very different types of stress: 13 ^°C, 33 ^°C,120 mM NaCl and 15% PEG-6000 water solutions. The four genes exercised no effect on root and hypocotyl elongation under the same stress conditions and their effect on plantlets growth varied depending on the genotype and the treatment. The usefulness of genes ah, aw, blsand al ₁ in breeding tomato and pepper cultivars tolerant to adverse climatic conditions at germination when used as a morphological marker, is discussed.