The research investigated the effect of dietary supplementation with Artemia sp. enriched with the autochthonous probiotic Enterococcus faecium on growth performance, microbiota modulation, intestinal morphology, and resistance to pathogenic bacteria of Megaleporinus macrocephalus larvae. The study evaluated four treatments (C: without probiotics; T1: 1 × 104 ; T2:1× 106 ; and T3: 1 × 108 CFU·mL-1) in quadruplicates. The larvae (n = 160; weight = 5.3 ± 2.3mg and length = 3.73±0.4mm) were distributed in 16 L containers at a density of 10 larvae·L-1 for 20 days. The productive performance, survival, gut microbiology, and histology were measured. The larvae were also submitted to acute challenge against the pathogenic bacterium Aeromonas hydrophila. The results showed that supplementation with 1 × 108 CFU·mL-1 promotes greater gain in length (13.78 ± 0.40 cm) and total weight (0.08 ± 0.002 g), higher counts of lactic acid bacteria and lower total heterotrophic in the intestines (7.11±0.30; 0.12 ± 0.09 log CFU·g-1, respectively) and larger villi (0.26 ± 0.03μm). Diets containing probiotics influenced the animals’ resistance to acute infection, with a lower accumulated mortality in T3 (33% ± 11.54%) and a higher one in C+ (93% ± 11.54%). Thus, probiotic supplementation with the autochthonous bacterium E. faecium (1×108CFU·mL-1) provides zootechnical improvement, villus increase and greater resistance to infections.