The deceased were Karim, 28 and Swapan, 24, sons of Kaladhan Sarkar of Ward No 8 of Guthuma municipality area.
Kaladhan said the duo went for fishing in the early hours today but did not return.
Assistant Superintendent of Police Nishan Chakma said the cause of their death is not clear yet as the bodies bore no injury marks.
Members of Border Guard Bangladesh (BGB) handed over the bodies to police in the afternoon after a flag meeting with Indian Border Security Force, he added.
The bodies were sent to Sadar Hospital for autopsy, he said.
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