Metagenomics experiments often characterize microbial communities by sequencing the ribosomal 16S and ITS regions. Taxonomy prediction is a fundamental step in such studies. The SINTAX algorithm predicts taxonomy by using k-mer similarity to identify the top hit in a reference database and provides bootstrap confidence for all ranks in the prediction. SINTAX achieves comparable or better accuracy to the RDP Naive Bayesian Classifier with a simpler algorithm that does not require training. Most tested methods are shown to have high rates of over-classification errors where novel taxa are incorrectly predicted to have known names.