The siblings were identified as Sumaiya, 13, and her brother Rimon, 4, children of Liton Sardar of Khaserchar under Memania union of Hizla upazila.
OC Masuduzzaman of Hizla police said the trawler capsized around 9pm on Thursday when Liton along with his wife and three children were trying to board on a Dhaka-bound moving launch.
The siblings had been missing since the capsizing.
The other people on the trawler were rescued immediately.
The rescue operation for the missing two siblings started following the accident.
Sumaiya’s body was recovered around 11:30am from Meghna River at Kaishma area under Barojaliya union, about 4 kilometers from Hizla.
Rimon’s body was recovered after an hour in the same area.
The bodies were handed over to the family members, police said.