Microalgae are a group of photosynthetic microorganisms living in the water. They are in the spotlight as biostimulators and biofertilizers in modern renewable and sustainable agriculture system, attributed to characteristics such as photosynthetic, and metabolism of various industrial wastes and to increase production when treating crops. Scenedesmus sp. CHK0059 is also one of the microalgae with these characteristics, and it has been reported to suppress various diseases in crops and promote the health of vegetables. However, the mode of action that has a positive effect on plants is not yet well understood. This study was designed to focus on the modulation in diversity change of plant microbiota community, which was the result of the preliminary study, and to determine the direct changes in microbial members that trigger the diversity change in the Arabidopsis model system. As a result, there was no change in the phenotype of Arabidopsis and the microbiota community structure in the rhizosphere during the treatment period, but two bacteria genera, Brevibacterium and Pseudomonas, dominance in the rhizosphere was positively correlated with the CHK0059 treatments. And the bacteria had a positive network correlative relationship with 24 other bacteria. Our findings suggest that the application of microalgae was correlated with several microbiota members in the rhizosphere and was expected to affect the microbiota community structure modification in long-term treatment.