Microarrays constructed with the genes encoding key enzymes involved in various biological and geochemical processes are referred to as functional gene arrays (FGAs), or GeoChip. On the basis of GeoChip 2.0 (He et al., 2007), 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) has been developed. GeoChip 3.0 has several new features compared to GeoChip 2.0. First, GeoChip 3.0 cover about 47,000 gene sequences for 292 gene families, and such a coverage allows us to obtain more information about microbial communities and analyze more diverse environmental samples. Second, the homology of automatically retrieved sequences by key words is verified by HUMMER using seed sequences so that any potential unrelated sequences are removed. Third, GeoChip 3.0 includes phylogenic markers, such as gyrB. 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 a complicated array, especially for future update. Fifth, universal standards have been implemented in GeoChip 3.0 so that data normalization and comparison of different samples can be conducted. Finally, genomic standards are also used to quantitatively analyze gene abundance. GeoChip was used to analyze effects of elevated CO2 on belowground microbial communities at BioCON. The results demonstrated that GeoChip 3.0 could 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.