Several groups of bacteria have the capacity to derive extra energy from light while still oxidizing organic matter for carbon and energy. Among these photoheterotrophs are the aerobic anoxygenic photosynthetic (AAP) bacteria, which harvest light energy with the use of bacteriochlorophyll a but do not evolve oxygen. The goals of this dissertation work were to determine ecological controls on the distribution of AAP bacteria in estuaries. In eight transects over five years, AAP abundance was measured in the Delaware and Chesapeake estuaries. Both microscopy and quantitative PCR (qPCR) data indicated that AAP bacteria comprised a large portion of the prokaryotic community in the estuaries examined. In the Delaware, AAP bacteria were on average 12% of bacteria, while in the Chesapeake they were less abundant, making up on average 6% of cells. As determined by qPCR, 0.6 to 50% of bacteria were AAP in the Delaware. In both estuaries, AAP abundance was inversely correlated with light, indicating they were particularly abundant in turbid waters. These results were surprising, since the photoheterotrophic capabilities of these bacteria should provide them with competitive advantages in environments with high light availability. To further examine the ecological implications of turbidity, I tested for AAP particle-attachment preferences. Up to 90% of AAP bacteria were attached to particles, while usually 20% or less of the total prokaryotic community was in the particle-attached fraction. By both microscopy and qPCR, it was determined that particle-attached AAP bacterial abundance estimates were positively correlated with seston concentrations (r=0.65, p<0.01 and r=0.68, p<0.01, respectively). These results suggest that estuarine types of AAP bacteria are particularly competitive in high-nutrient, turbid waters. To examine the potential ecological controls over subsets of the AAP bacterial community, I first examined metagenomic and PCR libraries for diversity of pufM, a photosynthesis reaction center gene common to all AAP bacteria. The metagenomic data revealed the presence of two distinct types of AAP bacteria in the Delaware River. Extensive phylogenetic analyses of light-harvesting and non-phototrophy genes suggested that the two types of AAP in the metagenomic data set occupy two distinct niches (freshwater and estuarine) in estuaries. To further examine the diversity of freshwater and estuarine types of AAP bacteria, I amplified the pufM genes from microbial consortia DNA harvested from the Delaware River. In two pufM libraries constructed from summer and winter samples, the most prevalent form of pufM was the freshwater ecotype, but the estuarine type of this gene was only a minor member of the AAP bacterial community. However, in a study of the actively expressed pufM genes in the river, the estuarine type was more important in the community, comprising 10% of the clones. The data from the metagenomic study and the PCR diversity study led to my hypothesis that two niches would be occupied by AAP bacteria containing these different types of genes. qPCR assays were then designed to target freshwater, estuarine, and marine types of AAP bacteria of the Delaware estuary, and the physical distribution of these three ecotypes were examined in four transects of the estuary in 2002-2004. In all samplings, both the freshwater and marine types were most abundant in the riverine and bay ends of the estuary, declining with water mixing. The estuarine type, however, did not follow consistent patterns. In summer, this type of pufM was more abundant in the bay, while it was shifted upstream into the freshwaters in the autumn and winter samples. Finally, to examine the particle-attached and free-living preferences among these three ecotypes of AAP bacteria, I examined their abundances in two size fractions. In the free-living fraction, all three ecotypes followed distribution patterns similar to those of the 2002-2004 transects. In contrast, the marine, freshwater, and estuarine ecotypes in whole water were most abundant in mid-estuary near the turbidity maximum. These data suggest that particle-attachment is a general phenomenon among dominant groups of AAP in the estuary. Overall, the data in this dissertation provide clues to the environmental adaptations of estuarine AAP bacteria, but more diversity and distribution studies are needed to further understand the ecological controls of AAP bacteria.