Abstract <p>The study was conducted to evaluate the efficiency of DNA extraction applied to different types of sunflower plant material using several kits for automated DNA extraction and purification. Twelve individual plants of the VK 678 line were analyzed. The experimental material included axial organs of the achene’s embryo, true green leaf, cotyledonary leaves of etiolated 7-day and 3-day seedlings. Each tissue type (1.2–5.1 mg sample) was obtained from 12 individual plants. The MagnoPrime FITO and MagnoPrime GMO reagent kits adapted for use on the Auto-Pure 96 automatic station for nucleic acid extraction and purification were used for DNA extraction. The quantity and quality of the isolated DNA were determined spectrophotometrically. The extraction kit, the type of plant material, and the interaction of these two factors had a reliable effect on the concentration of nucleic acids at the 5% significance level. When using the MagnoPrime FITO kit, the concentration of the nucleic acid solution extracted from the axial organs of the achene’s embryo and true green leaf varied in the ranges of 59.67–142.66 ng/μL and 43.38–209.01 ng/μL, respectively. There was no contamination with proteins and phenols in these variants, and the A260/A280 ratio was within the optimal values of 1.81–2.13 units. The use of the MagnoPrime GMO kit ensured a high concentration of nucleic acids in the solution isolated from the axial organs of the achene’s embryo (95.92–140.38 ng/μL). These DNA samples were also not contaminated with proteins, and the optical density ratio A260/A280 was 1.96–2.05. The best results in terms of speed, cost-effectiveness, concentration, and purity of isolated DNA were achieved with extraction from the axial organs of the achene’s embryo using the MagnoPrime FITO kit.</p>