Microarrays fabricated with the genes encoding key, functional enzymes involved in various biological and geochemical cycling processes are referred to as functional gene arrays (FGAs). Based on GeoChip 2.0, which contains 24,243 oligonucleotide (50mer) probes and covers > 10,000 gene sequences in >150 functional groups involved in nitrogen, carbon, sulfur and phosphorus cycling, metal reduction and resistance, and organic contaminant degradation, a new generation of GeoChip (GeoChip 3.0) is being developed. GeoChip 3.0 has several new features compared to GeoChip 2.0. First, GeoChip 3.0 is expected to cover >37,000 gene sequences of 290 gene families, and such a coverage allows us to obtain more information about microbial communities and analyze more diverse environmental samples. Second, GeoChip 3.0 includes phylogenic markers, such as gyrB. Third, the homology of automatically retrieved sequences by key words is verified by HUMMER using seed sequences so that unrelated sequences are removed. Fourth, a software package (including databases) has been developed for sequence retrieval, probe and array design, probe verification, array construction, array data analysis, information storage, and automatic update, which greatly facilitate the management of such complicated array, especially for future update. Finally, GeoChip 3.0 also includes GeoChip 2.0 probes, and those GeoChip 2.0 probes are checked against new databases. Disqualified probes are flagged. GeoChip 3.0 will provide more capability for studying biogeochemical processes and functional activities of microbial communities important to human health, agriculture, energy, global climate change, ecosystem management, and environmental cleanup and restoration. It is also particularly useful for providing direct linkages of microbial genes/populations to ecosystem processes and functions.