We investigated the impact of the Deepwater Horizon oil spill on microbial communities in wetland sediment and seawater samples collected from sites along the Gulf shore. Based on GC/MS analysis, the sediment from Bay Jimmy, LA had detectable signs of hydrocarbon contamination, identified as n-alkanes in the GC/MS spectrum similar to that of the Deepwater Horizon source oil (MC-252). To identify changes in microbial assemblage structure and functional diversity in response to hydrocarbon contamination, five genes (bacterial 16S rRNA, Pseudomonas-specific 16S rRNA, alkB, P450, and PAH-RHDα) were selected based on the specific enzymes encoded by bacteria to degrade alkanes or polycyclic aromatic hydrocarbons. A quantitative PCR analysis revealed the presence of alkane and PAH-degrading genes in both contaminated and non-contaminated samples with no significant difference in gene content between contaminated and non-contaminated samples. However, the ribotype analysis based on pyrosequencing identified 17 bacteria genera known for their capacity to degrade hydrocarbons, including Mycobacterium, Novosphingobium, Parvibaculum, Pseudomonas, and Sphingomonas, in the contaminated sediment sample. Furthermore, the contaminated sample had a very high relative abundance of 16S rRNA gene sequences affiliated with the genus Parvibaculum, members of which have been characterized for their degradative abilities. These data suggest that specific bacterial taxa within the genus Parvibaculum have the capacity for hydrocarbon degradation and could use the hydrocarbons as a carbon and energy source, resulting in a dominant population in a hydrocarbon-contaminated soil. In summary, when exposed to the spilled oil, the distinct wetland microbial communities responded with decreased diversity and increased abundance of selective degradative species.