The GeoChip arrays have been shown to be powerful tools in linking microbial function to ecosystem processes and are able to provide sensitive, specific, and potentially quantitative information. Use of this array in bioremediation studies have expanded our understanding of the microbial processes and communities at work in these sites and provide information necessary for the successful improvement and application of bioremediation strategies. Over the past decade, great improvements have been made in regards to microarray technology, design, and application. However, there are still technical hurdles that need to be overcome to further improve sensitivity and specificity in addition to better methods of nucleic acid extraction and purification. Improved bioinformatics tools are also needed to assist with data processing and analysis.