According to police the duo was arrested from Buraburi village in the Mayong police station area of the district and another person who had allegedly shot the rhino was still absconding.
An adult male rhino was killed by poachers inside the heavily flooded Sanctuary on the night of July 4.
The poachers came by a boat and killed the rhino before fleeing away along with its horn.
Large parts of the Sanctuary have been under flood water since the past one week and most of the animals in the Sanctuary have fled to higher grounds.
The 38.8 km Sanctuary, located about 30 km east of Guwahati, has a dense population of around 93 Great Indian one-horned rhinoceros in 16 sq km of its effective rhino habitat.
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