Bacteria of the Burkholderia cepacia complex (BCC) are associated with severe infection in cystic fibrosis. Recent evidence shows that the mucoid phenotype is common in BCC bacteria; however, during chronic infection, transitions from the mucoid to nonmucoid morphology have been shown to take place. Here we use RNA microarray and proteomic isobaric tagging relative and absolute quantitation technologies to gain insight into a pair of mucoid and nonmucoid isolates of B. cenocepacia obtained from a chronically infected patient with cystic fibrosis in the year prior to her death. During chronic infection, the mucoid isolate lost the B. cepacia epidemic strain marker and acquired a mutation in the cepR gene. In the nonmucoid isolate, we observed overexpression at both the RNA and protein level of several described putative virulence factors, including a nematocidal protein AidA and the oxidative stress response protein AhpC. We show that this translates into increased resistance to oxidative stress in the nonmucoid isolate, a key microbial determinant for resistance against phagocytic cell killing. These data illuminate the biological differences between mucoid and nonmucoid BCC bacteria, provide targets for elucidating the genetic control of exopolysaccharide production in the BCC, and highlight that chronic infection can produce both genetically and phenotypically distinct microbial variants in the cystic fibrosis lung.