The world is reaching a point where effectiveness of antibiotics could be completely com- promised in the near future, if antimicrobial resistance (AMR) continues to spread globally. The intestinal microbiota of human and domestic animals is suspected to be the main reser- voir of AMR organisms and therefore of antibiotic resistance genes (ARGs). Advances in DNA sequencing technology and more specially metagenomic approaches have shown that several ARGs are prevalent and shared between most gut microbiota. Although nucleotide diversity is documented for many ARGs, each variant following independent spread, the dis- tribution of theses variants in gut resistomes is still completely unknown. This study aims to understand if ARGs described as identical in different microbiomes are actually the same variants. We adapted DESMAN, an algorithm developed to reconstruct strains from metagenomic data, to characterize different variants from a pool of ARGs. The tool was applied to ARGs detected in metagenomic cecal samples from chicken raised under different condi- tions. Among 22 genes analyzed, 15 have at least 2 stable variants, 7 (ant(6), blaTEM-1 , erm(B), erm(F), tet(Q), tet(L) and tet(32)) showing variants with important differences in proportions between samples depending on rearing condition and age of animals. Sequence comparison between variants reconstructed by DESMAN and those identified from bacterial isolates revealed a perfect match. These results attest the reliability of the tool to recon- struct different variants of the same ARG directly from metagenomic data and to infer their relative proportion in different samples. It opens the way for futher analysis to understand their relative abondance, persistence and transmission between microbiomes.