Assistant police inspector D V Jadhav of Mumbra police station said the accused, who were embroidery workers, lived in Amrtunagar area.
Ismail Mohamad Gous Sayyed (34) allegedly raped his elder daughter, while his brother Aslam Mohamad Gous Sayyed (23) raped her younger sister first in November last year. They allegedly raped the girls later too.
The offence was registered yesterday when the victims' mother approached the police.
A local court remanded the two brothers in police custody till November 21.