Incongruence between gene trees is the main challenge faced by phylogeneticists in the genomic era. Incongruence can occur for artefactual reasons, when we fail to recover the correct gene trees, or for biological reasons, when true gene trees are actually distinct from each other, and from the species tree. Horizontal gene transfers (HGTs) between genomes are an important process of bacterial evolution resulting in a substantial amount of phylogenetic conflicts between gene trees. We argue that the (bacterial) species tree is still a meaningful scientific concept even in the case of HGTs, and that reconstructing it is still a valid goal. We tentatively assess the amount of phylogenetic incongruence caused by HGTs in bacteria by comparing bacterial datasets to a metazoan dataset in which transfers are presumably very scarce or absent.We review existing phylogenomic methods and their ability to return to the user, both the vertical (speciation/extinction history) and horizontal (gene transfers) phylogenetic signals.