The firm recently announced its intention to close in January 2008 following the sale of its parent to Mothercare.
The sites - owned by Waterstone and Scottish publisher DC Thomson under Chelsea Stores Holdings - are being sold to Mothercare, along with sister company, Early Learning Centre. The deal is expected to complete on 19th June.
DC Thomson has retained intellectual property rights to the brand, and plans to relaunch the chain.
"When we agreed to sell ELC to Mothercare, we lost the Daisy and Tom sites," Waterstone said. "We will start all over again. The new stores will be smaller, with more own-brand products, and sales will be more internet-driven. But the brand will definitely survive."
Daisy and Tom was launched by Waterstone 10 years ago. At its height, it had six stores turning over around £15m a year. It now has just two in Chelsea and Dublin, with the sale of its Guildford branch under way.