The interest in the use of antimicrobial peptides to control fungal diseases in banana plants has been rising in the last years. In this paper we analyzed the antifungal activity of different peptides on the in vitro development of Mycosphaerella fijiensis and found that they inhibited fungal mycelial growth and ascospore germination. All peptides evaluated displayed activity against the fungus although with marked differences in IC50 values ranging between 3.06 and 239.61 µg/mL. The peptides exhibiting better activity were the designated peptides Ib-AMP4 and Ib-AMP2, both derived from Impatiens balsamina. Furthermore, the in vitro activity of these peptides seemed compatible with existing chemical fungicides, having no antagonistic or synergistic effect with these agents. The effect of these peptides on M. fijiensis mycelial elongation and ascospores germination suggests that they can be used as potential alternative strategies for the control of black Sigatoka disease.