Microarray technology, used in microorganisms detection with its advantages of rapid detection, high sensitivity, high-throughput and low cost, has been applied in environmental microbial community research widely in past few years. It focuses on investigation of structure, diversity, function, dynamics of microbial populations within complex environmental samples. Furthermore, it also reveals their responses and adaptation to environmental perturbations such as climate change, toxic contaminants. According probe design patterns, several types of microarrays, such as phylogenetic oligonucleotide arrays (POAs), functional gene arrays (FGAs), metagenomic array(MGA) and community genome arrays (CGAs) have been constructed for environmental studies. This review discusses applications of microarrays to environmental microbial populations research along with its potential for screening of specific microorganisms, gene or expression functional gene representing different environmental microbial populations.