Virgin Atlantic and British Airways have cancelled Heathrow-Miami services this lunchtime due to Hurricane Matthew.
A BA flights from Miami to Heathrow tonight have also been cancelled. Dozens of US domestic services from the Florida airport are also affected.
Virgin Atlantic waived rebooking fees for two days for passengers travelling to and from Miami and Orlando.
The move came as Florida and South Carolina prepared for the hurricane which has let a trail of devastation across Haiti and is heading towards the Bahamas and forced travel companies to re-arrange flights.
US president Barack Obama warned that the coming days would be dangerous and urged the public to heed official advice.
Florida governor Rick Scott said his state could be facing its biggest evacuation ever. South Carolina governor Nikki Haley said 250,000 people would be evacuated from coastal areas.
At least 16 people are believed to have been killed by Hurricane Matthew so far, including four killed by collapsing walls and mudslides in the Dominican Republic.
Dozens of homes in the eastern city of Baracoa in Cuba were destroyed.
Virgin Atlantic said: “Due to the forecast weather conditions from Hurricane Matthew, customers booked to travel to, from and through Miami and Orlando on 6 and 7 October 2016 who prefer to rebook may do so, without penalty.
“Rebooking is subject to availability in the same booking class for flights and travel must be completed on or before 12 October 2016.”
Thomas Cook said it was resuming flights today to and from Holguin in eastern Cuba, saying there is no damage to hotels after the hurricane passed through the island.
This followed the re-routing flights on Monday and Tuesday to Cayo Coco where alternative accommodation was found after Holguin airport was shut down on Sunday. The company had 1,500 holidaymakers in Holguin on Sunday.
Cook, the largest UK operator in Cuba, moved 570 holidaymakers due to fly home on Monday and Tuesday to the nearest airport at Cayo Coco.
Group head of customer welfare, Carol MacKenzie, said: “Hurricane Matthew has now passed through Cuba. We are in the process of making an assessment of the damage and speaking to all our customers.
“We are still in the process of contacting everyone but so far, reports indicate they are safe and well.
“We are now monitoring our flights to Florida which are currently operating as scheduled, although we cannot guarantee that there will be no disruption due to the unpredictability of the weather.
“We understand how worrying the hurricane has been for our customers and their family and friends back home. Please be assured we did everything possible to ensure everyone’s safety – that’s always our highest priority.”
All of the operator’s flights to and from Orlando today until, Saturday are currently due to operate on schedule as is a Miami service today.
People due to travel over the next two days have been advised to call Cook’s customer service line on 01733 224 536. Thomson said flights today from Birmingham and Manchester to Sanford in Florida are due to depart as scheduled.
“Thomson Airways is closely monitoring the development of Hurricane Matthew, which is forecast to affect Florida,” the company said.
“Our dedicated team in Florida are working with the relevant authorities and hoteliers to ensure everyone is looked after and kept updated with the latest information and advice.
“We will continue to monitor the situation closely and we encourage customers to check our website for updates. Alternatively, they can contact us on 0203 636 1997 for more information.”
Matthew is the region’s most powerful hurricane since Felix in 2007.