In this work we studied in vitro the antifungal effect of essential oils obtained from the Greek flora aromatic plants of the Lamiaceae family, Satureja horvatii ssp. macrophylla, Coridothymus capitatus, and Origanum vulgare ssp. hirtum, on two phytopathogenic fungi, which cause black spot of tomato fruits (Alternaria sp.) and potato tuber dry rot (Fusarium sp.) during storage. According to the results of Gas Chromatographic–Mass Spectrometry analysis, the essential oils of S. horvatii ssp. macrophylla, C. capitatus, and O. vulgare ssp. hirtum used in the experiments belong to the carvacrol chemotype. The antifungal effect of the essential oils on the phytopathogenic fungi was evaluated by fumigant assay. An essential oil-free treatment was used as a control. After 8 days of fungal growth on the Petri dish, the results showed that some of the essential oils completely inhibited the mycelial growth of the phytopathogenic fungi Fusarium sp. and A. alternata. This effect could be further evaluated in vivo for the fruits' post-harvest protection from phytopathogenic fungi during storage, aiming to improve agricultural products' quality.