Left back Mohanraj spent the first two ISL seasons with Atletico de Kolkata and won the tournament in 2014. He joins Chennaiyin on a free transfer after the expiry of his contract at ATK.
Central midfielder Ganesh was signed by Chennaiyin on loan from Pune FC last season after being the first draft pick of CFC in the 2015 ISL domestic player draft.
But Ganesh suffered an ACL injury while on India team duty in September 2015 and thus missed the entire ISL. Chennaiyin have now signed him on a permanent basis.
"Ganesh was very unlucky to be injured last year. We hope to have him at his best this season. Mohanraj is already an ISL winner and has the quality to make a big difference in our title defence," said Chennaiyin FC head coach Marco Materazzi.
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He was also India captain at U-19 level and had his first professional contract at HAL Bangalore before moving to Kolkata giants Mohun Bagan, where he spent five years.
Mohanraj also had a spell at Pune FC and had been part of the India senior national team setup under Bob Houghton since 2008 with the senior international debut coming in March 2011 during the 2012 AFC Challenge Cup qualifiers.
"I have been playing professional football for almost a decade now and finally my dream of playing for a club in Chennai is coming true. I would like to thank all the Chennaiyin FC owners and head coach Marco Materazzi for believing in me. I can't wait to put on the Chennaiyin jersey and play at the Marina Arena in front of our fans. Winning the ISL with ATK was great but lifting the trophy as a Chennaiyin player will be extra special and I am going to work very hard to achieve that," said an emotional Mohanraj.
The 25-year-old made his senior India debut in June 2015 and regularly featured in current India coach Stephen Constantine's plans before suffering an unfortunate ACL injury during a match against Iran last September.