The present study was carried out to investigate the protective effect of short chain fatty acids (acetic, propionic and butyric acids) on gnotobiotic Artemia franciscana nauplii against the shrimp pathogen Vibrio harveyii. The antibacterial effect of different concentrations (1, 10 and 100mM) of individual short chain fatty acids against V. harveyii was determined by bacterial growth study at pH 6. At 100mM concentration of all the tested short chain fatty acids, the pathogen growth was completely inhibited. The pH (5-7) dependent growth inhibition of 20mM concentration of short chain fatty acids against V. harveyii was determined by bacterial growth study. At pH 5, the pathogen growth was highly inhibited in all the tested short chain fatty acids. The Artemia nauplii (instar II) gnotobiotically reared in 20 mM short chain fatty acids supplemented medium were challenged with V. harveyi, and the mortality was recorded at an interval of 6 h up to 60 h. In this study, the reduction in mortality of Artemia nauplii was 36.95, 30.05 and 24.15%, respectively in acetic acid, propionic acid and bytyric acid. The present results provide justification for short chain fatty acids as alternative antibiotic in aquaculture against shrimp pathogen V. harveyii.