Johannes Smuts was the only child of Johannes J.L. Smuts, a prominent citizen of Cape Town, and his first wife Cornelia G. Fleck. The younger Johannes studied at the Rijksuniversiteit (State University) at Leiden, The Netherlands, where he was awarded a doctoral degree in philosophy and the natural sciences in 1832. His thesis, Dissertatio zoologica inauguralis, exhibens enumerationem mammalium capensium... (Zoological doctoral dissertation, with a summary of Cape mammals) was written in Latin in accordance with the requirements of Dutch universities at the time. Published in Leiden in 1832 (110p), it was the first scientific publication dealing exclusively with the South African fauna. It consisted mainly of a systematic account of the mammals of the Cape Colony, divided into orders, families and species. Much remained to be discovered at the time, so that his descriptions were rather brief and incomplete. For example, in the last chapter, dealing with the order Cetacea (marine mammals), he identified only five species of whales with certainty. The published thesis included a farewell poem by a friend, Hermann Schlegel, after whom Smuts had named Meriones schlegelii (the Cape Gerbil, now Tatera afra).
Soon after his graduation Smuts returned to Cape Town. On 20 March 1833 he married Susanna M. Ferris, with whom he had five daughters and seven sons. In various almanacs for 1835 to 1838 he was described as a "naturalist, seedsman, etc" or "collector of curiosities", with a garden in Oranje Street, a "museum of natural curiosities, seeds, etc", and stores in St George's Street (De Jong, 1985/6, p. 122 Note 3). By 1857 he was living at Zorgwyk, the residence of his father in Gardens. When he died in 1869, at the same address, he had no occupation and possessed only clothes and books.
The naturalist Johannes Smuts should not be confused with his cousin (a son of his father's youngest brother), also named Johannes Smuts (1819-1871), who qualified in medicine at Leiden in 1843 and practiced in Paarl for many years.