Abstract Two transcribed genes encoding 3-ketoacyl-CoA thiolase [(EC 126.96.36.199) Thiolase III], one of the peroxisomal thiolase isozymes, of n-alkane-utilizable yeast, Candida tropicalis, were isolated. Restriction maps of these two genes were very similar. Each of the genes had only one open reading frame consisting of 1224 bp corresponding to 408 amino acid residues. The nucleotide sequences of another thiolase isozyme in peroxisomes of C. tropicalis, acetoacetyl-CoA thiolase (Thiolase IA and IB), have been already determined (Kurihara et al., Eur. J. Biochem., 210, 999–1005, 1992). The amino acid sequences of these peroxisomal thiolase isozymes (Thiolases I and III) showed 35% homology. The regulation of biosynthesis of these thiolases in C. tropicalis was compared by RNA and Western blotting analyses. The results revealed that the biosynthesis of Thiolase III in C. tropicalis was strongly induced in a medium containing butyrate or alkanes as a carbon source and a peroxisome proliferator, while Thiolase I was constitutively expressed even in a medium with glucose or acetate, although a slight induction was observed at the levels of transcription and translation in the medium containing butyrate or alkanes. Thus, the regulations of biosyntheses of Thiolases I and III were found to be quite different, in spite of the enzymes in the final step of the peroxisomal fatty acid β-oxidation system.