Botanical Journal of the North Caucasus was founded by the Mountain Botanical Garden of the Dagestan Scientific Center of RAS in 2013 (the first certificate of registration of mass media PI No. FS 77-55933 dated 11/07/2013). In 2013, the journal received the international registration number ISSN 2409-2444. In 2020, due to the reorganization of the Dagestan Scientific Center and the change of the founder of the journal, a new certificate of registration of the media PI No. FS 77-79583 dated December 7, 2020 was received. The founder is the Dagestan Federal Research Center of the Russian Academy of Sciences.

In 2020, there was a change in the periodicity of the journal from four to two issues per year.

In 2021, "Herald" was replaced by "Journal" in the English title of the journal – the Botanical Journal of the North Caucasus.