Different types of antimicrobial peptides has been identified in seeds from different species of plants, among them are defensins, thionins and LTPs. The aim of this work was to isolate peptides presents in chili pepper seeds (Capsicum annuum L.) and evaluate their antimicrobial activities against some yeast species. Meal from these seeds was prepared and peptides were extracted in phosphate buffer (Na₂HPO₄ 10 mM, NaH₂PO₄ 15 mM, KCl 100 mM, EDTA 1.5 %, pH 5.4) in a 1:10 rate (meal:buffer) for 3 h at 4 ºC. The supernatant obtained after the extraction was submitted to a precipitation with 90 % relative ammonium sulfate saturation, the precipitate was ressuspended in distilled water and heated at 80 ºC for 15 min. The resulting suspension was clarified by centrifugation and the supernatant was extensively dialyzed against distilled water followed by purification employing ion-exchange chromatography on CM-Sepharose column. The purification process was monitored by Tris-Tricine/SDS gel electrophoresis. Three peptide enriched fractions, namely F1Ca, F2Ca and F3Ca, were obtained after the CM-Sepharose chromatography. The chili pepper crude extract (F-0/90) exhibited strong fungicidal activity against several yeast species tested. The fraction F3Ca, mainly composed of three peptides of 6-10 kDa, obtained after cation exchange chromatography and eluted with 0.2 M of salt, present inhibitory activity against the yeasts Saccharomyces cerevisiae, Candida albicans, Candida tropicalis, Pichia membranifaciens, Candida guilliermondii, Kluyveromyces marxiannus and Candida parapsilosis. Some morphological changes in the cells also could be observed, as well the ability to form pseudohyphae and increase of the bud number. This F3Ca fraction also inhibited the glucose-stimulated acidification of the medium by the yeast Saccharomyces cerevisiae in a dose-dependent manner.