The shortfin silverside (Chirostoma humboldtianum) is a native fish of central Mexico with high value for artisanal fisheries. So far, attempts aimed to establish intensive culturing have failed. In this study, we evaluated the effect of probiotic strains; Bifidobacterium animalis subsp. lactis BB-12, Lactobacillus johnsonii C4, and Bacillus sp. B2 bio-encapsulated into Artemia franciscana on Chirostoma humboldtianum weight and length. Their influence on the fish intestinal bacterial communities was also assessed. The final weight and final length of the fishes fed with bio-encapsulated Bifidobacterium animalis BB-12, and L. johnsonii C4 were statistically different and higher than the control group. According to PCR-DGGE fingerprints of 16S rRNA gene, the intestinal content bacterial community associated with the shortfin silverside seems to be molded in early larval stages and only slight changes could be induced by the use of bio-encapsulated bacterial. An increase in fish survival rate and an improvement in weight and length were detected using L. johnsonii C4 bioencapsulated into A. franciscana, in spite of its small impact on the structure of the bacterial community associated with the intestinal content of shortfin silverside. The use of L. johnsonii C4 bio-encapsulated into A. franciscana could be an excellent option to improve the yield during intensive culturing of the shortfin silverside.