In a series of tweets, Aditya Thackeray, son of Sena chief Uddhav Thackeray, blamed "egos of vested" interests for the break-up of the 25-year-old alliance.
"Very sad that State BJP chose to part ways with 25 yr old ally Shiv Sena when we stuck together even in their bure din, unconditionally (sic)," said one of the tweets.
He said that the alliance had faced many challenges together and the vested interest were kept at bay.
"This alliance has seen many ups and downs, challenges and protests, but we faced it together. Vested interests were kept at bay.
"Even as of now, we and many in the Maharashtra BJP do regret that vested interests have prevailed over unity, pre-elections. I hope sense prevails over vested interests, soon," Aditya, who heads the Yuva Sena, said in another tweet.
The Thackeray scion said that the party supported Narendra Modi for his development vision and ideology despite the 2002 Gujarat riots.
"It was for development n ideology that we supported @narendramodi ji in 2002 and now at the center," he tweeted.
He also blamed the "vested interests" who were unhappy when he went to talk to the BJP over the seat-sharing agreement. Thackeray, 24, was one of the negotiators who represented the party in talks.
"Ego of vested interests saw my age than the effort. For the last 5 days, I purposely chose not to comment on it, as for some State BJP leaders my age was more important than my effort for unity," another tweet said.
Sending out an emotional message, he said the alliance was formed by his grandfather Bal Thackeray and Pramod Mahajan even before his birth and for him it was like a family that he grew up with.
"This alliance of Shiv Sena and @BJP4India was forged by hon'ble Balasaheb Thackeray and Pramod kaka for ideology and development. For me, and many in SS-BJP, this isn't a political alliance but family forged by my Grandfather n Pramod kaka, Atalji and dvaniji
"This alliance has been since before I was born. I have grown up in an atmosphere of unity with BJP leaders and members, so many memories! This is the unity and family bonding I have seen since childhood. That little boy, me, always a witness to this."