While it has been shown that phytoplankton productivity and community structure are influenced by the availability of Fe in several high nutrient–low chlorophyll (HNLC) regions of the world's oceans, the influence of Fe on the bacterial community remains unresolved. Therefore, we sampled water from the Peruvian upwelling region of the equatorial Pacific Ocean and examined how bacterial community structure changes with Fe additions (1.5 nM, 0.5 nM above ambient) and sequestration, which was accomplished by additions of the fungal siderophore desferrioxamine B (DFB) (1.0 nM, 5.0 nM). We hypothesized that either 1) the bacterial communities are generally Fe-limited and thus show positive responses to Fe addition; or 2) that bacteria form the equivalent of response groups and show a limited number of responses to Fe addition; or else 3) that the bacterial communities show no response to Fe addition. Using Terminal Restriction Fragment Length Polymorphism analysis, we found that the eubacterial community changed in response to Fe. Whereas the overall community shows little abundance and richness responses to Fe availability, bacteria can be arranged into response groups showing divergent responses to Fe addition. With validated cluster analysis, we found that the bacterial community consisted of four response groups. One group showed strong positive responses to increasing Fe availability, while another group showed strong negative responses. The abundance patterns of the final two groups showed no response to alterations in Fe availability, although one persisted at a high abundances and the other a low abundance. These results reveal that it may be difficult to describe a singular bacterial community response to changes in Fe availability, and that understanding the influence of Fe on bacteria dynamics may require an understanding of the different responses of individual sub-groups of bacteria within the microbial community.