Propolis is known to have biological properties against numerous microorganisms of clinical interest. This study aimed to determine the chemical composition and antifungal activity of Brazilian propolis (types 3 and 13) against Candida spp. and their effects on the morphology of preformed and mature Candida biofilms. Samples of propolis (3 and 13) collected by Apis mellifera honeybees were obtained from different regions in Brazil. Ethanolic extracts of propolis (EEP) were prepared, fractionated and submitted to chemical analysis by GC/MS. The extracts and their hexane, dichloromethane and ethyl acetate fractions were tested for their ability to inhibit Candida spp. (C. albicans, C. dubliniensis, C. glabrata, C. kruzei, C. tropicalis and C. parapsilosis) by determination of the minimum inhibitory and fungicidal concentrations (MIC/MFC). Additionally, their effects on morphology of preformed and mature biofilms were observed by scanning electron microscopy. The phenolic compounds p-coumaric acid, caffeic acid phenethyl ester (CAPE), kaempferol and quercetin were identified in the EEP-3 and its bioactive dichloromethane fraction; and isoflavonoids such as medicarpin, vestitol and formononetin were found in the EEP-13, and triterpenes in its bioactive hexane fraction. The EEP-3 and EEP-13 and their bioactive fractions showed MIC values ranging from 0.2 to 125 μg/mL and MFC values between 125 and 500 μg/mL. The EEP and fractions were predominantly fungistatic agents. All extracts and fractions disrupted biofilm structures at 500 μg/mL and amorphous areas with cell damage were clearly observed in preformed and mature biofilms. Propolis types 3 and 13 have strong anti-Candida activity and should be considered as promising candidates to treat oral and systemic candidiasis.