The presence of lysine (Lys) or arginine (Arg) and tryptophan (Trp) are important for the antimicrobial effects of cationic peptides. Therefore, we designed and synthesized a series of antimicrobial peptides with various numbers of Lys (or Arg) and Trp repeats [(KW and RW)(n)-NH(2), where n equals 2, 3, 4, or 5]. Antifungal activities of these peptides increased with chain length. Light microscopy demonstrated that longer peptides (n = 4, 5) strongly inhibited in vitro growth of Fusarium solani, and Fusarium oxysporum, at 4-32 μM. Furthermore, longer peptides displayed potent fungicidal activities against a variety of agronomical important filamentous fungi, including F. solani and F. oxysporum, at their minimal inhibitory concentrations (MICs). However, RW series peptides showed slightly higher fungicidal activities than KW peptides against the two strains. Taken together, the results of this study indicate that these short peptides would be good candidates for use as synthetic or transgenic antifungal agents.