The deceased were identified as Ratan Mia, 35, and Monira, 5.
Officer-in-Charge (OC) of Kalmakanda Police Station said the bodies were found from separate places of Haldi Bil in Dharmapasha upazila.
Police already arrested five staff members of the trawler, although they are still for the driver who has been on the run, the OC said.
Abdul Wahab, husband of one of the deceased earlier filed a case in this regard.
It means twelve people, including six minors and three women, drowned after the trawler capsized on Gumai River on Wednesday morning.
Also read: 11 dead in Netrakona trawler capsize