Defining bacterial species is difficult due to frequent horizontal gene transfer (HGT) across species and even lineages albeit with diverse frequency.To investigate constraints of HGT and function-relevant genes and sequence variations involved,we discover a hierarchical organization of lineage-associated variations (LAVs) of core genomes across lineages of eubacterial taxa,based on genomic sequences of E.coli strains from diverse geographic origins.We further find that the LAVs of higher taxa appear restricting HGT among lineages of the lower taxa and thus provide distinct species and lineage barriers.