Botanists at the Royal Botanic Garden Edinburgh (RBGE) reached the milestone - dubbed B2K - 268 years after the first species was described.
The landmark discovery, together with partner scientists in Asia, the Americas and in Edinburgh, is part of the race to catalogue life on Earth in the face of the biodiversity crisis.
The Begonia is one of the world’s largest flowering plant genera, first described 268 years ago in 1753 by the Swedish "father of modern taxonomy", Carl Linnaeus.
Once decried as a "repulsive" bedding plant by gardening guru Monty Don much is still to be learned about its evolution and distribution in the wild.
Dr Mark Hughes, a tropical botanist at the RBGE, said: "To record the 2000th species of Begonia is a major accomplishment in a long-term project which not only involves cultivating and recording species new to science but also poring over historic records for others that have been missed or misidentified over the generations.
"While herbarium and archive records here at RBGE, and at our partner organisations around the world are significant, there are challenges in streamlining the various banks of information.
"In particular, many of the older species’ names were published in rare journals. These and their associated specimens need to be traced and verified as part of our wider research.
"With improvements in technology and information sharing, and a more coordinated approach, we are now seeing real dividends."
Over the last decade, substantial progress has been made in Begonia studies, with between 50 and 100 species being added each year.
They have included species that are striking to the eye, fragile, bizarre, critically endangered and even the smallest ever found.
In addition to new species, botanists have rediscovered some unseen for nearly two centuries.
Dr Hughes said: "During an expedition to North Sumatra, Indonesia, in late 2018, colleagues from Bogor Botanical Gardens, Java, found an unusual Begonia in the forests near Lake Toba.
"Since then, we have been undertaking a joint investigation and, from examining meticulous records dating back to 1822, we are now in no doubt we have Begonia fasciculata. Not a new species, but one that has not been recorded as living for nearly 200 years.
"This species was described as new to science by the indefatigable William Jack, a polymath who graduated from Aberdeen University at the age of 16... Many of the species Jack described have not been recorded growing anywhere since."
The first Begonia identified was Begonia obliqua, published in 1753 by Linnaeus, who formalised the modern system of naming organisms.
The name was coined by French botanist Plumier in honour of his benefactor Michel Begon, at the port of Rochefort, in south-western France.
By the end of the 18th century a handful of Begonia species had been formally described.
The first to be described by an Edinburgh botanist was Begonia dipetala from India, in 1828, by then RBGE Regius Keeper Robert Graham.
Naming a "new" plant can be a slow process. One example, Begonia korthalsiana, was first collected in Sumatra in 1872 and only formally described in 2015.