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Reception
The book, first published in French in 1813, was reissued in 1819 and soon translated to German by Kurt Sprengel, who expanded on the ideas presented in the book in respect to the structure of plants and also included his own ideas about the distribution of plants. In 1821, the German translation was translated to English, and the English translator noted that the textbook successfully documents the recent advances in botany and represents both the current wealth of established knowledge and the very latest emerging theories in plant science at the time. A year later, in 1820 de Candolle would publish one of his most significant works, "Essai élémentaire de géographie botanique" which contained information on biogeography not found in any of his previous works, with the exception of the German translation by Sprengel, in where Sprengel expanded on these ideas based loosely on Candolle’s ones.

The reception for the book was positive, with de Candolle being considered one of the "founding fathers" of natural systematics thanks to this work, in which he introduced a new classification system and the term taxonomy. Beyond the field of biology, the book was well received by some notable people of the time, such as Jean-Baptiste Say, who wrote a letter to de Candolle telling him that his book put him "amongst the best philosophers", and William Whewell, who quoted de Candolle on several occasions.

After the first publication in 1813, de Candolle received criticisms from proponents of intelligent design for dealing with the problem of useless organs in plants. The critics claimed that his argument would embolden and give arguments to the proponents of the world as a product of chance. In the 1819 edition, de Candolle addresses this issue by claiming that these "mistakes" in the designs of plants can help as evidence for intelligent design, as they can function as a way to achieve symmetry. Charles Darwin later criticized these ideas, claiming that: "At a period not far distant, naturalists will hear with surprise, perhaps with derision, that grave and learned men formerly maintained that such useless organs were not remnants retained by inheritance, but were specially created and arranged in their proper places like dishes on a table (this is the simile of a distinguished botanist) by an Omnipotent hand to complete the scheme of nature." In the third edition of the book, published by Alphonse de Candolle (de Candolle’s son) in 1844, a footnote mentions that the corresponding pages for the argument were crossed out by his father, indicating that his father had intention to change them.

From 1813 to his death in 1841, de Candolle continued to form and refine his new botanical classification system which was established in Théorie Élémentaire de la Botanique. In 1824, de Candolle began the publication of the collection, Prodromus Systematis Naturalis Regni Vegetabilis, a summary of all plant types known at the time along with their characteristics, including taxonomy, evolutionary history, and biogeography. He completed the first seven volumes of the total seventeen of this collection prior to his death. Despite not completing his goal for the collection, he characterized more than 100 plant families in this process, which became a base for the field of studying general botany. The final ten volumes were completed by de Candolle's son, Alphonse Pyramus de Candolle, with the seventeenth published in 1873.