GM petunias were identified first in Finland in April after Helsinki University asked the Finnish government agency to investigate petunias they suspected had been modified.
After they were identified in Finland, the Horticultural Trades Association said it expected the orange varieties would be in the UK.
Instructions to growers and garden centres are to take them off the market and destroy them. Thompson & Morgan and Mr Fothergill's are among those who have confirmed they hae withdrawn plants for sale. Takii
There is a reported 55m petunias produced annually worldwide, with around 5m being orange.
APHA said inspectors there are no human health or environmental issues, but because they are unauthorised GM plants, they cannot be grown or sold in the the EU. Sources suggest tens of thousands have been thrown away so far.
Dutch food safety agency RIKILT has also confirmed GM in Go!Tunia Orange, Sanguna Salmon, Viva Orange, Viva Fire, Viva Orange and African Sunset, but not in Cascadias Indian Summer or Sanguna Patio Salmon.
USDA confirmed GM petunias were in the USA earlier in May, while in Finland, agency Evira said they were initally confirmed in late April.
African Sunset breeder the Japanese-owned Takii was waiting for confirmation of Dutch tests but Takii Europe managing director Ton Kuipers said as a "precautionary action ... we have blocked all the sales and have approached all the customers from the past year to see if they still have any in stock to ask them to send them back to us".