Butyrate is a short chain fatty acid with important industrial applications currently produced by chemical synthesis. With increasing consumer demand for green products, the fermentative production of butyric acid by microorganisms such as Clostridium is attracting interest. Clostridium butyricum naturally ferments non-digested dietary fibre in the colon to produce butyrate which has multiple health benefits, and certain strains are used as probiotics such as MIYAIRI588 (CBM588). Acquiring knowledge of the genes encoding enzymes involved in the butyrate production pathway in CBM588, and determining those that are rate-limiting due to low concentrations, could enable strain engineering for higher yields to create an enhanced probiotic or for direct product extraction. To this end whole genome sequencing of CBM588 was performed. Annotation revealed a circular chromosome of 3806640 bp harbouring 3349 protein-coding genes, 88 tRNA genes and 30 rRNA genes, a megaplasmid of 794389 bp harbouring 736 protein-coding genes including Cas genes of a CRISPR-Cas system and the previously reported cryptic plasmid, pCBM588. The genome closely matched C. butyricum strain KNU-L09. All genes involved in the butyrate production pathway were found on the chromosome. To identify rate-limiting steps, the relative abundance of the encoded enzymes was assessed by liquid chromatography-mass spectrometry (LC-MS) of total cytosolic proteins. Phosphotransbutyrylase (Ptb) was the least abundant closely followed by butyrate kinase (Buk) and crotonase (Crt). Analysis of upstream regulatory sequences revealed the potential importance of an intact Shine-Dalgarno sequence. Results of this study can now guide bioengineering experiments to improve butyrate yields and potentially enhance the performance of CBM588 as a probiotic.