Shrimp has been among the top value-added products targeted for production by the aquaculture industry. The increasing demand for shrimp has led to a massive increase in production in several countries across the world. Intensive and super-intensive production systems are facing great challenges handling newly emerging shrimp diseases. The use of antibiotics was one of the first approaches when dealing with such diseases, but the effects of misusing antibiotics and the appearance of antibiotic resistant bacteria are of public concern. As an alternative, probiotics have been applied in aquaculture systems to increase disease resistance, improve feed efficiency, maintain water quality and enhance the growth of aquatic organisms. In this study, the ability of three probiotic microbes to tolerate salinity levels commonly found in intensive shrimp production systems were evaluated. Lactobacillus casei, Saccharomyces cerevisiae and Rhodopseudomonas palustris were cultured in MRS broth, yeast and mold broth, and Van Neil’s broth, respectively, enriched with 1 and 2% NaCl. Microbial survival between treatments were compared as well as the metabolic activity in terms of acidity levels. Additionally, cell morphology was compared using scanning electron microscopy. L. casei and S. cerevisiae showed no significant differences (P>0.05) in media with 1% and 2% NaCl in terms of microbial survival and media acidity levels at 24 h. R. palustris showed a prolonged lag phase extending up to 12 h in 1% and 48 h in 2% NaCl media, and acidity of the media did not vary significantly. Cell morphology of all microbes did not change significantly across all treatments. From these results, it was concluded that L. casei, S. cerevisiae and R. palustris are suitable for application in aquaculture ponds with up to 2% salinity.