Synthetic fertilizers are widely employed in agriculture relative to biofertilizers. Long-term use affects soil fertility, plant vigor, human and livestock health, and the soil microbial community. Seaweeds were employed as biofertilizers in sustainable agriculture to overcome this issue and boost the agricultural productivity. Therefore, the current study investigates the effect of wheat seeds priming with the aqueous extracts of Ulva linza or Corallina officinalis seaweeds at various concentrations (5, 10, 15, 20, and 30%). Wheat grains were primed with seaweed extracts and grown in petri dishes, and the germination rate, growth attributes, physiological parameters, cytological traits, and molecular analyses were evaluated. The physico-chemical characterization revealed that U. linza possessed higher levels of ash, soluble proteins, and sugars, as well as essential macronutrients and amino acids, than C. officinalis. Seedling growth parameters, physiological characteristics, and mitotic index all showed a substantial increase in low concentrations of both extracts when compared to the control. Higher concentrations, on the other hand, exhibited an inhibitory effect as well as certain chromosomal abnormalities. In the treated seedlings, new proteins were expressed, which could be owing to the activity of bioactive components in the extracts. As compared to untreated seedlings, PCR-RAPD analysis utilizing five markers revealed that both seaweed extracts triggered low and high molecular weight DNA fragments, as well as fragments specific to each extract. Seaweed extracts could be employed as an environmentally friendly and soil-safe alternative to typical chemical fertilizers.