Background The objective of this study was to compare the level differences of mRNA transcription and protein expression of PPARγ, FAS and HSL in different parts of the carcass in different tail-type sheep. Six Tan sheep and six Shaanbei fine-wool sheep aged 9 months were slaughtered and samples were collected from the tail adipose, subcutaneous adipose, and longissimus dorsi muscle. The levels of mRNA transcription and protein expression of the target genes in these tissues were determined by real-time quantitative PCR and western blot analyses. Results The results showed that PPARγ, FAS, and HSL were expressed with spatial differences in tail adipose, subcutaneous adipose and longissimus dorsi muscle of Tan sheep and Shaanbei fine-wool sheep. Differences were also observed between the two breeds. The mRNA transcription levels of these genes were somewhat consistent with their protein expression levels. Conclusion The present results indicated that PPARγ, FAS and HSL are correlated with fat deposition, especially for the regulating of adipose deposition in intramuscular fat, and that the mRNA expression patterns are similar to the protein expression patterns. The mechanism requires clarification in further studies.