This work aims to investigate the effect of cultivation method on phytochemical profile and antifungal activities of essential oils gained from cultivated and wild fennel seeds and herb in Turkey. Wildly obtained fennel had lower dry, fresh herb and seed yield than cultivated fennel. By contrast, essential oil content of fennel herb and seeds was significantly reduced when fennel was grown under field conditions compared to wild. In total, 50 compounds representing more than 98% of the essential oils were identified. Estragole, fenchone and limonene have found as the major components both wild and domesticated plants. However, the proportions of the components varied significantly based on cultivation and plant samples. Estragole were found 55.08% and 73.69% for herb and 48.29% and 57.57% for seed oil for the wild and cultivated plants, respectively. While the fenchone contents of herbs and seeds were similar in both plants, limonene content in domesticated plants decreased from 22.43% to 1.48% for seed and 7.54%–2.01% for herb essential oils. The examined oil has shown a low to moderate fungal development inhibition capability against F. oxysporum and B. cineria especially high concentrations. Biocontrol efficiency of herb essential oils in both plants was higher than the seed essential oils.