We have previously shown that Saccharomyces cerevisiae mitochondria contain a full set of mitochondrial DNA-coded isoaccepting tRNAs. We report here the presence of two lysine tRNA isoacceptors in purified yeast mitochondria, only one of which (tRNA2Lys) is of mitochondrial origin. The other mitochondria-associated lysine tRNA (tRNA,Lys) does not hybridize with mitochondrial DNA (mtDNA) and elutes with one of the cytoplasmic lysine tRNA isoacceptors in the RPC-5 column chromatographic system. This tRNA was purified by two-dimensional polyacrylamide gel electrophoresis of in vivo 32P-labeled total mitochondrial tRNA. Sequence analysis showed that it corresponds to cytoplasmic tRNALys (anticodon C-U-U), whose primary structure has already been determined by Smith and coworkers [Smith, C. J., Teh, H. S., Ley, A., & D'Obrenan, P. (1973) J. Biol. Chem. 248, 4475-4485], tRNA,Lys is present in tRNA preparations extracted from RNase-treated mito chondria as well as from submitochondrial fractions, such as inner-membrane or mitosol preparations. It is absent in the mitochondrial outer-membrane preparation. These results show that the presence of tRNA1Lys in mitochondria is not a result of cytoplasmic contamination and suggest strongly that it is imported from the cytoplasm. This cytoplasmic tRNA seems not to be involved in the transfer of lysine into mtDNA-coded polypeptide chains since (1) it is not acylated by the mitochondrial aminoacyl-tRNA ligase preparation and (2) mtDNA-coded mitochondrial tRNA2Lys recognizes both lysine codons. It is postulated that the presence of tRNA1Lwys in yeast mitochondria results from active transport involving a specific receptor (other than mitochondrial lysyl-tRNA ligase). This tRNA may have a regulatory role, and its function could give an important insight into the relationship between the mitochondrial and the nuclear-cytoplasmic systems. © 1979, American Chemical Society. All rights reserved.