The one-day, statewide strike was called by the Kerala unit of the United Forum of Bank Unions (UFBU), an umbrella organisation of nine banking sector unions.
The employees took out morchas across the state demanding that the centre give up the merger move to avoid adversely affecting the interests of depositors and employees of LKB and the social banking cause.
While the strike affected the functioning of public sector and scheduled banks, the new generation banks were functioning normally, officials said.