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Crop management should be determined to reintroduce ancient wheat. This study aimed to determine: i. the response of the yield of ancient wheat on sowing density; ii. the impact of sowing density on plant health, weed infestation and pest occurrence. Field experiments were carried out in Poland, on three organic farms. The factors were: (1) wheat species: Persian wheat (Triticum persicum Vav.) and Indian dwarf wheat (T. sphaerococcum Perc.), (2) sowing density (400, 500, and 600 grains m−2). Increasing the sowing density of T. sphaerococcum from 400 to 600 grains m−2 increases the grain yield and reduces the pest pressure (Oulema spp. and Aphididae). Sowing densities did not affect the severity of powdery mildew at stem elongation as well as root rot and eyespot at the development of fruit. At the highest sowing density, the leaf area with tan spot symptoms was the highest. The eyespot symptoms occurred more frequently and the damaged plant surface caused by Oulema spp. was larger on T. sphaerococcum. Persian wheat turned out to be more susceptible to weed infestation. Indian dwarf wheat and Persian wheat are useful for organic farming, and the sowing density should be 500 or 600 grains m−2 and 400 grains m−2, respectively.