The boat was carrying around 90 passengers when it began to keel over after it was hit by massive waves, prompting a rescue operation that stretched into the night and left authorities scrambling to react.
The body of a man wearing a life jacket with the logo of the Phoenix boat was pulled from the sea.
Footage on the public relations Facebook page Phuket showed the body brought to shore.
The governor of southern Phuket, Noraphat Plodthong, said 49 people -- over half of the passengers -- were still "being helped" as rescue boats rushed to the scene.
A second provincial official, requesting anonymity, told AFP rescuers "are working to find" the 49 missing.
Television footage taken at a pier in Phuket showed stunned tourists huddling in blankets, while several women cried as medics tended to the injured.
The boat was returning to Phuket from Koh Racha at around 4:00 pm (0900 GMT) when a storm hit, according to the captain, who identified himself as Somjing Boontham in a televised interview.
He said the boat was hit by five metre-high waves, which flooded the boat and started to slowly keel over, prompting him to warn passengers to put on life jackets and trigger inflatable life rafts.
"So I sent someone to them to wear life jackets... They were all Chinese visitors -- apart from two farang," he said using Thai vernacular for westerners, adding around half the passengers were unaccounted for.
Phuket is a magnet for overseas visitors including Western sun-seekers and Chinese tourists who will make up the bulk of the 35 million people expected to visit the kingdom this year.
Governor Noraphat said Phuket officials had issued a weather warning on Wednesday alerting the public about impending storms.
"There were high winds this evening," he said, adding a further 10 pleasure boats were stranded at sea and being attended to by rescue boats from the police and navy.
Others who made it to shore were covered in blankets and being tended to by medics at a pier in Phuket, several women cried and shouted in what sounded like Chinese.
Two other separate boat capsizes were reported in the same area Thursday evening.
A yacht called the Senerita carrying 39 people also capsized in the high seas, the officials added.
All of the passengers in both cases were pulled from the sea alive.
Photographs circulating on social media showed soaked and exhausted passengers -- most of them Asian -- in life jackets being pulled on inflatable rafts to safety.
It was not immediately clear which boat they belonged to.
Thailand has a sketchy health and safety record and accidents are common on its roads and busy waterways - especially during the monsoon season which is now biting.
The kingdom is already in the global spotlight for a dramatic rescue mission in the north of the country, after 12 boys and their football coach were trapped in a cave complex.
Eyewitness? Submit your stories now via social or:
Email: eyewitness@pulse.ng
![The woman was recorded, among others, while bathing [BI]](data:image/svg+xml;charset=utf8,%3Csvg%20xmlns%3D'http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg'%20width%3D'300'%20height%3D'172'%20data-ring-placeholder%3D'1'%3E%3C%2Fsvg%3E "The woman was recorded, among others, while bathing [BI]")
