Abstract: Functional gene arrays (FGAs) can detect and analyse the population structure, community dynamics and functional activity of microorganism in biomining in a rapid, accurate and high-through-put manner, thus help the monitoring of microorganism’s growth and metabolism and the rapid screening of microorganism with high-efficient biomining capacity. This paper introduces the characteristics of functional gene array and its applications in ecological and functional analysis of biomining microorganism, and finally discusses the existing main problems and the application prospect of this technology.