Eukaryotes typically utilize two distinct aminoacyl-tRNA synthetase isoforms, one for cytosolic and one for mitochondrial protein synthesis. However, the genome of budding yeast (Saccharomyces cerevisiae) contains only one cysteinyl-tRNA synthetase gene (YNL247W, also known as CRS1). In this study, we report that CRS1 encodes both cytosolic and mitochondrial isoforms. The 5 complementary DNA end method and GFP reporter gene analyses indicated that yeast CRS1 expression yields two classes of mRNAs through alternative transcription starts: a long mRNA containing a mitochondrial targeting sequence and a short mRNA lacking this targeting sequence. We found that the mitochondrial Crs1 is the product of translation from the first initiation AUG codon on the long mRNA, whereas the cytosolic Crs1 is produced from the second in-frame AUG codon on the short mRNA. Genetic analysis and a ChIP assay revealed that the transcription factor heme activator protein (Hap) complex, which is involved in mitochondrial biogenesis, determines the transcription start sites of the CRS1 gene. We also noted that Hap complex-dependent initiation is regulated according to the needs of mitochondrial energy production. The results of our study indicate energy-dependent initiation of alternative transcription of CRS1 that results in production of two Crs1 isoforms, a finding that suggests Crs1's potential involvement in mitochondrial energy metabolism in yeast. Aminoacyl-tRNA synthetase (ARS) 2 is an ancestral housekeeping enzyme found in all organisms. ARSs are essential for This work was supported in part by Grants-in-Aid for Scientific Research (S), (B), and (C) and for Young Scientists (B) 18H04794 and 18H02621 (to H. M.), 15K21759 and 18H05277 (to T. A.), 17K08619 (to T. I.), and 17K15408 (to A. N.) and Grant-in-Aid for Scientific Research on Innovative Areas 26111008 (to T. A.) from the Ministry of Education, Sciences, Sports, and Technology (MEXT) Japan and by AMED under Grants JP19gm5010002 (to H. M.) and JP18fm0208029 (to T. A.). The authors declare that they have no conflicts of interest with the contents of this article. This article contains Figs. S1-S4, Tables S1 and S2, and experimental procedures.