Soil microorganism is one of the most important factors in evaluating and improving soil quality because they play a crucial role in the soil material circulation. They are closely correlated with soil environmental factors, and in particular, soil pH has a significant impact on the microbial community. This study aimed to examine the relationship between microbial communities and soil pH in orchard soil of the Republic of Korea. Microbial communities of 63 sites with neutral soil pH (pH 6 -7) and 26 sites with acidic soil pH (pH 3 -5) were analyzed targeting 16S rRNA and ITS genes through Illumina Miseq platform. Our analyses showed that bacterial richness and diversity and fungal richness in neutral soil were significantly higher than those in acidic soil (p < 0.001). According to PCoA and PERMANOVA, the microbial communities were significantly different in two soil groups, and ANCOM-BC showed high abundance of 16 bacterial and 15 fungal genera in neutral soil. Lastly, 9 genera, including Terrimonas, Povalibacter and Gp taxa, were identified as hub genera that have a significant impact on other microbial taxa in neutral soil. These results indicated that soil pH is a critical determinant of microbial communities and can serve as an indicator soil quality monitoring and evaluation.