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The utilization of marine algae as potential sources of pharmaceutical agents has been increasing recently, due to the realization that they contain bioactive compounds, which inhibit the growth of some pathogenic bacteria, as well as some yeasts. The aim of this work was to establish an improved procedure for obtaining extracts from marine algae, and to test the antimicrobial activity of these extracts against selected species of yeasts, Gram-negative and Gram-positive bacteria. Seaweeds used in this study were obtained in the North of Portugal, from integrated aquaculture. Gracilaria vermiculophylla was used for the preliminary assays of optimization of the extraction procedure, whereas Gracilaria vermiculophylla, Porphyra dioica and Chondrus crispus were used for antimicrobial assays. Optimization studies were focused on the definition of the pre-treatments of the algae (drying), and the temperature and type of solvents used during the extraction process. Results revealed that test organisms were more sensitive to extracts obtained with dried algae, continuously processed at higher temperatures. Concerning antimicrobial capacity evaluation, species tested were: Gram-negative - Escherichia coli, Salmonella enteritidis, Pseudomonas aeruginosa; Gram-positive: Listeria innocua, Bacillus cereus, Enterococcus faecalis, Lactobacillus brevis, Staphylococcus aureus, all from food origin and a strain of Staphylococcus aureus from clinical origin. The yeast Candida spp. was from clinical origin as well. Tests to assess the antimicrobial activity of the extracts were performed using the agar diffusion method, and results indicated a stronger antimicrobial activity of the ethyl acetate extracts, when compared with methanolic or diethyl ether extracts.