Microarrays allow the examination of thousands of genes at one time without the need for PCR amplification of each gene. Since microarrays were first shown to be valuable for the study of microbial communities (Guschin et al., 1997) , several types have been designed to examine microbial communities. These include (i) phylogenetic oligonucleotide arrays (POA), designed to examine phylogenetic relatedness or community composition using 16S rRNA or other conserved phylogenetic genes (Small et al., 2001; Loy et al., 2002; Wilson et al., 2002; Brodie et al., 2006) ; (ii) community genome arrays (CGA), designed to examine the relatedness of microbial species or strains or to identify community members using whole-genomic DNA probes Zhang et al., 2004) ; (iii) metagenomic arrays (MGA), designed as a highthroughput screening method using environmental clone library inserts as probes (Sebat et al., 2003; Mockler and Ecker, 2005; Gresham et al., 2008) ; (iv) whole-genome ORF arrays (WGA), designed to examine gene expression of individual microorganisms using probes for all ORFs in one or more genomes (Wilson et al., 1999) , but can also be used for comparative genomics (Murray et al., 2001) ; and (v) functional gene arrays (FGAs), designed to examine multiple functional genes at one time using probes for key genes involved in microbial functional processes of interest He et al., 2007 He et al., , 2010a . This review will focus on FGAs.