The supermarket's Leckford Farm, Hampshire, will cultivate the ancient varieties, some of which have never been grown commercially in the UK before.
Six varieties will grow on 3,000 trees and the RHS helped choose apples that would grow well and produce good crops.
Ashmeads Kernel, Adams Pearmain, Pixie, Sunset, Chivers Delight and Kidd's Orange Red fruit throughout the season. Peak harvests will hit the 80-tonne mark.
Leckford Farm fruit specialist Tom Palmer said: "We have taken advice to ensure the varieties are sustainable and have wide appeal."
The trees began life through rootstocks that were grafted into budding wood, said Waitrose senior fruit buyer Jocelyn Clarke. Leckford Farm has committed 10ha of land.
Clarke said: "During the season we aim to source 70 per cent of apples from the UK. Leckford's collection will increase volumes and varieties of traditional apples in Waitrose."