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We present an RNA-Seq based approach to map 3′ end sequences of mature 16S rRNA (3′ TAIL) in bacteria with single-base specificity. Our results show that 3′ TAILs are heterogeneous among species; they contain the core CCUCC anti-Shine-Dalgarno motif, but vary in downstream lengths. Importantly, our findings rectify the mis-annotated 16S rRNAs in 11 out of 13 bacterial species studied herein (covering Cyanobacteria, Deinococcus-Thermus, Firmicutes, Proteobacteria, Tenericutes, and Spirochaetes). Furthermore, our results show that species-specific 3′ TAIL boundaries are retained due to their high complementarity with preferred Shine-Dalgarno sequences, suggesting that 3′ TAIL bases downstream of the canonical CCUCC motif play a more important role in translation initiation than previously reported.