The 16S rRNA gene is widely used for bacterial phylogenetics, species delineation, and microbiome research. Historically, researchers assumed that sequence variations in this gene were only due to speciation and inheritance. But there are reports of recombination events and an unreliable phylogenetic signal. To examine this directly, researchers performed four intra-genus analyses and one inter-genus analysis using pathogenic and core human microbiome genera. In all analyses, the 16S rRNA gene was recombinant and subject to horizontal gene transfer. At the intra-genus level, the 16S rRNA gene averaged 50.7% concordance with the species phylogeny, one of the lowest of the core genes. Further analysis found that the single nucleotide polymorphism (SNP) count was a major factor influencing concordance. 690 ± 110 SNPs would be required to reach 80% concordance, but the average SNP count for the 16S rRNA gene was only 254. The 16S rRNA gene performed better at the inter-genus level, reaching 70% concordance when the whole gene was used, but the most concordant hypervariable regions of the gene only reached 62.5% concordance. Due to the common usage of this gene in phylogenetic and microbiome research, the ramifications of its poor performance are far reaching, and the use of such approaches without incorporating other phylogenetic information should be discouraged.