The filamentous fungus Aspergillus niger has been used for the production of citric acid for nearly a century.  Strain selection has resulted in changes in growth and metabolism that were most favorable to processing.  A. niger strains currently available are capable of highly efficient conversion, processing 90% of available sugars into citric acid.  Improvements to production were obtained through a process of selection that ultimately resulted in a strain with altered morphology and metabolism.  Routine growth of A. niger includes the formation of long branching hyphae.  In citric acid production, rather than developing long filaments, compact clumps of hyphae form small pellets. This pelleted growth is a contributing factor in the ability to produce citric acid.  However, changes in metabolism must also have occurred that account for the large conversion of glucose into citric acid.  Tools for investigating this organism have expanded since the genome sequence from two different strains of A. niger became publically available. We examined citric acid production in A. niger using genomics, cell biology and proteomics.  Through the study of A. niger and citric acid production, we hope to develop tools that will aid in exploitation of other fungi in the production of fuels and chemicals.