Apicidin is a cyclic tetrapeptide produced by some Fusarium species and is known to inhibit Apicomplexan histone deacetylase. The goals of this study were to determine species identity of Fusarium isolate KCTC16676, an apicidin producer, to improve a method for apicidin extraction, and to test phytotoxicity of apicidin and its analogs. We compared sequences of the translation elongation factor 1-alpha (TEF) gene in KCTC16676 with those from isolates representing diverse Fusarium species, which showed that KCTC16676 belongs to the F. semitectum-F. equiseti species complex. To enhance apicidin production, after culturing isolate KCTC16676 on a wheat medium for 3 weeks at 25oC, the culture was extracted with chloroform. Apicidins were purified through a reverse phase C18 silica gel column, resulting in 5 g of apicidin, 200 mg of apicidin A, and 300 mg of apicidin D2 from 4 kg of wheat cultures; this represents a significant yield improvement from a previous method, offers more materials to study the modes of its action, and facilitates the elucidation of the apicidin biosynthesis pathway. Apicidin and apicidin D2 showed phytotoxicity on both seedlings and 2-week-old plants of diverse species, and weeds were more sensitive to apicidins than vegetables