Brine shrimp (Artemia spp.) is a significant factor in determining aquaculture production. Since the microbiota of Artemia can colonize the gut in larvae, various microorganisms transmitted from Artemia can affect host larval health. Although the microbiota composition of Artemia would be essential in determining aquaculture productivity, our understanding on microbiome of Artemia is still insufficient. Through our study, we identified the species of Artemia cysts supplied by three different manufacturers (P1, P2, and P3) with investigation of size and hatching efficiency. The species of Artemia from P1 was identified as A. tibetiana, and P2 and P3 was A. franciscana. A. tibetiana hatched from the P1 cysts had the largest body size with the lowest hatching rate. Furthermore, we conducted a comprehensive analysis of the microbiome present in the rearing water and the nauplius whole body from each product. We observed specific microbiota compositions, both beneficial and harmful, depending on the product types and the sample types. Additionally, we found that the microbiota composition in the rearing water was associated with the manufacturing environment, while the compositions in the nauplius whole body were species-specific. Notably, we discovered that an extract containing microbiota from the nauplius sample of P3 increased the hatching rate of A. tibetiana, indicating a positive role in Artemia culture. These findings demonstrate that the microbial communities present in Artemia vary according to the product and/or species, underscoring their significance in aquaculture production.