Premlata and Sonia, both in their 20s and relatives, were found in a pool of blood in the building in Wazirabad area.
The police suspect Premlata's husband Mohit could have a role in the killings. He has been missing since the matter was reported to them.
It is suspected that Mohit had a fight with his wife last night and killed her, said a police official, adding that it could be possible that when Sonia tried to intervene he killed her too.
Sonia recently underwent a surgery and Premlata and Mohit came to stay with her to take care of her.
The incident came to light when Sonia's father's calls to the women went unanswered and he asked his tenant, who stays upstairs, to enquire about them.
The tenant went downstairs, found the bodies and informed the police.