Various plant metabolites have therapeutical properties and have widely been used in traditional and western medicine. Low cost, availability as well as the need for natural remedies led to an increase in research focused on the use of medicinal plants. In Puerto Rico (PR), medicinal plants are widely used however; the therapeutic capacity of Puerto Rican flora has not been amply explored. Our goal is to define the biologically active compounds in aqueous extracts of five medicinal plants from PR, Psidium guajava, Annona muricata, Lippia stoechadifolia, Mentha nemerosa and Mentha X. Piperita. These plants are commonly used as home remedies to treat symptoms of respiratory or gastrointestinal diseases. Moreover, we aim to determine the anti-microbial activities of these plants against the microorganisms Streptococcus pneumonia and Streptococcus pyogenes (pneumonia) as well as Salmonella enteritidis and Campylobacter jejuni (gastroenteritis). Phytochemical screenings showed that P. guajava, L. stoechadifolia, and M. nemerosa were positive for Tannins, Saponnins, Cardiac Glycosides, Alkaloids and Terpenoids; M. X. Piperita was positive for Tannins, Saponnins, Alkaloids, Steroids and Cardiac Glycosides, while A. muricata was positive for Terpenoids. Our data suggest that P. guajava, L. stoechadifolia, and M. nemerosa have the highest anti-bacterial potential. Surprisingly, when bacteria were treated with the above extracts no anti-bacterial function was observed. Plates without bacteria incubation and plates with bacteria but no extract treatment were used as positive control and negative control respectively. Quantitative tests of the phytochemical compounds are imperative to further investigate the lack of anti-bacterial activity under these experimental conditions.