The species of genus Baccharis spp. (Compositae) are an important natural resource in the search for new bioactive compounds. This article presents an investigation of volatile compounds of two species of Baccharis that are native to southern Brazil (Baccharis dentata (Vell.) G.M. Barroso and Baccharis uncinella DC) collected in summer and autumn of 2011. The essential oils were extracted by steam distillation and analyzed by gas chromatography-mass spectrometry (GC-MS), olfactometry analysis (GC-O) and qualitative assessment of the antimicrobial potential using the indirect bioautography method against Staphylococcus aureus, Salmonella enterica subspecie enterica serovar Choleraesuis, Pseudomonas aeruginosa, Candida albicans, Aspergillus niger, Candida parapsilosis, Cryptococcus neoformans, Rhizopus stolonifer, Fusarium solani and Aspergillus oryzae. The results demonstrated that the harvest period has an influence on the composition of the essential oils, but little influence on extraction yield. It can also be observed that the joint analysis of GC-MS and GC-O resulted in complementary information about the essential oils studied because the intensities of volatile compounds detected by both methods are significantly different. Regarding antimicrobial assays, it was found that the essential oil of B. dentata was effective against S. aureus, A. niger, C. parapsilosis and R. stolonifer, whereas the essential oil of B. uncinella was effective against S. aureus, S. Choleraesuis, C. albicans, A. niger, C. parapsilosis, R. stolonifer and F. solani.