The extensive use of antibiotics in intensive livestock production has contributed significantly to the emergence and spread of antimicrobial resistance, which constitutes a major global public health concern. Indicator bacteria such as Escherichia coli and Enterococcus spp. are commonly used to assess fecal contamination and to reflect the selective pressure exerted by antimicrobial agents on the gastrointestinal microbiota of food-producing animals. The aim of this study was to map the “microbial footprint” and evaluate antibiotic selective pressure in pig and laying hen farms in the Arta region of Western Greece through a comparative analysis of resistance patterns in E. coli and Enterococcus isolates. The results revealed widespread antimicrobial resistance across all samples. E. coli isolates from pig farms exhibited particularly high levels of multidrug resistance, with MAR index values ranging from 0.53 to 0.62, indicating intense and sustained antibiotic pressure. Enterococcus spp. displayed lower but consistently elevated resistance, especially to sulfonamides. Overall, the findings demonstrate that antimicrobial resistance is a stable characteristic shaped by bacterial species and farm management practices, underscoring the need for systematic surveillance and rational antibiotic use in livestock production systems.