The objective of this work was to evaluate the efficiency of the stabilization process of swine manure in storage ponds regarding the presence and antibiotic resistance of pathogenic bacteria. The study was carried out in two trials in ten swine farms located in the municipality of Presidente Castello Branco, in the state of Santa Catarina, Brazil. In the first trial, the efficiency in reducing Escherichia coli (EC), non-E. coli coliforms, and Salmonella sp., as well as the resistance of isolates to antimicrobials, was investigated under recommended handling conditions. Sampling was done at three depths and two times. In the second trial, the concentration of total and fecal coliforms (EC) was evaluated under field handling conditions, when the manure was distributed on the field. Sampling depth does not influence the concentration of EC and Salmonella sp., and isolated bacteria are multi resistant to the evaluated antibiotics. Hydraulic retention time is determinant in reducing the population levels of the indicator agents. The obtained results are indicative that swine manure handling must be carried out according to sanitary standards, in order to minimize the propagation risk and antimicrobial resistance of pathogenic microorganisms.