With the aim of finding new natural products for the protection of fruits against the pathogenic species responsible for fruit rot, the essential oil and the hydrosol extract of the root parts of Centaurea acaulis L. were tested for their antifungal activities against the species of Penicillium digitatum (Pers.) Sacc. and Penicillium italicum Wehmer, (1894) responsible for mold on oranges. The GC and GC/MS chromatographic profiles of the essential oil and the hydrosol extract revealed the existence of 15 and 21 components, respectively. Aplotaxene (60.3%) was the dominant compound in the essential oil, while the hydrosol extract was rich in sesquiterpene compounds, including caryophyllene oxide (36.2%) and veridiflorol (12.8%). The hydrosol extract of C. acaulis showed good antifungal activity against the two strains of molds P. italicum and P. digitatum with inhibition percentages of 84.5% and 75.3%, respectively. In addition, the in vivo antifungal activity test showed that washing oranges with the hydrosol extract showed a protective effect against orange mold caused by the two fungal strains with a percentage exceeding 93%. According to the results of the present study, the root hydrosol extract of C. acaulis can possibly be exploited as a natural agent for the protection of oranges against mold caused by P. italicum and P. digitatum.