Significance Pyrrolysyl-tRNA synthetase (PylRS) and its cognate tRNA ^Pyl have emerged as ideal translation components for genetic code innovation. We found that a series of PylRS variants that were initially selected to be specific for the posttranslational modification N ^ε -acetyl- l -Lys displayed polyspecificity [i.e., activity with a broad range of noncanonical amino acid (ncAA) substrates]. Our structural and biochemical data indicate that the engineered tRNA synthetases can accommodate ncAA substrates in multiple binding modes. The data further suggest that in vivo selections do not produce optimally specific tRNA synthetases and that translation fidelity will become an increasingly dominant factor in expanding the genetic code far beyond 20 amino acids.