There are two primary branches of the family, Khoikhoi of Namibia and South Africa, and Tshu–Khwe of Botswana and Zimbabwe.
Tom Güldemann believes agro-pastoralist people speaking the Khoe–Kwadi proto-language entered modern-day Botswana about 2000 years ago from the northeast (that is, from the direction of the modern Sandawe), where they had likely acquired agriculture from the expanding Bantu, at a time when the Kalahari was more amenable to agriculture.
The ancestors of the Kwadi (and perhaps the Damara) continued west, whereas those who settled in the Kalahari absorbed speakers of Juu languages.
These immigrants were ancestral to the north-eastern Kalahari peoples (Eastern Tshu–Khwe branch linguistically), whereas Juu neighbours (or perhaps Kxʼa neighbours more generally) to the southwest who shifted to Khoe were ancestral to the Western Tshu–Khwe branch.
However, the relationship has some predictive value, for example if the back-vowel constraint, which operates in the Khoe languages but not in Sandawe, is taken into account.
Counting each dialect cluster as a unit results in nine Khoe languages: Khoekhoe Eini† Khoemana (Korana, Griqua) Shua Tsoa ?
[4] It is not presently possible to say which languages correspond to which names mentioned in the anthropological literature, though the majority will likely turn out to be Shua or Tshua.