Because HGT of a specific piece of DNA depends on the relative concentrations of DNA fragments in the environment, the frequency of antibiotic resistance genes in a population is germane to any assessment of the potential of HGT of antibiotic resistance marker genes.

The prevalence of antibiotic resistant microorganisms in natural populations is high. For example, when researchers sampled municipal water supplies in Oregon and found, on average, 34% of the bacteria were resistant to multiple antibiotics. Because antibiotic resistance is often found in non-antibiotic producing soil microorganisms, this suggests that these genes were selected for because they allowed certain microorganisms to resist antibiotics produced by competitors in their environment.

Scientists have concluded that the presence of antibiotic resistance genes is so ubiquitous, it is highly unlikely that the introduction of biotech plants with antibiotic resistance marker genes will alter the frequency or distribution of these genes.