Cytoplasmic rRNA from the yeast mutant, mod5-1 is deficient in the modified base isopentenyladenosine and consequently migrates differently from isopentenylated wild type tRNAs on certain chromatographic systems. To determine if the mod5-1 mutation affects mitochondrial tRNA structure, the migration of mitochondrial tRNA from mod5-1 and wild type cells has been compared by reverse-phase chromatography. We conclude from this analysis that the single nuclear mutation that affects the isopentenylation of cytoplasmic tRNA also affects the isopentenylation of mitochondrial tRNA.