The application of animal waste from large-scale production facilities to cropland is a common means of manure disposal and nutrient recycling.  In addition to the high nutrient load, antibiotic residues and antibiotic-resistant bacteria enter into the environment through this process.  As yet, it is unclear how land application of waste can affect the occurrence and persistence of antibiotic resistance genes in natural environments.  To investigate the molecular ecology of resistance genes in soils with and without exposure to swine effluent, we monitored the frequency and distribution of 13 genes encoding tetracycline (tet) resistance and four genes encoding tylosin (erm) resistance using PCR methods. The metagenomic frequency and diversity of tet and erm genes were significantly higher in soil exposed to effluent than in soils without exposure. To correlate the occurrence of the resistance genes in the soil metagenome to the active microbial community, over 100 bacterial isolates with tetracycline- or tylosin-resistance phenotypes were obtained.  Identification based on 16S rRNA gene sequences revealed phylogenetically diverse bacteria commonly found in soil with primary associations to members of the phyla Proteobacteria and Bacteroidetes.  Numerous isolates harbored multiple tet genes and further, different tet genes were found in highly related strains, suggesting horizontal movement of genes. Only tet genes encoding an efflux mechanism of resistance were detected in the isolates, along with ermB. As expected, fewer antibiotic resistant isolates were obtained from soils with no history of effluent exposure.  While isolates recovered from soils without known effluent impact were phylogenetically similar to those found in impacted soils, the tet determinants between the two populations were distinctly different.  This study suggests that natural soil microbial populations can harbor a diversity of antibiotic resistance genes, however, exposure to swine effluent may increase the frequency and diversity of antibiotic resistance genes among the extant soil population.