Buyout firms Blackstone and CVC Capital Partners, which co-owned the company as majority shareholders until it floated the group in 2013, offloaded another chunk of stock worth £653m.
Deutsche Bank placed about 156m shares with investors at 417p a share, in an accelerated book building.
Shares were placed at a 2.2 per cent discount to the company’s closing price on Monday night.
Sources had suggested late on Monday that the bank was struggling to place the block trade, but Deutsche came through successfully to close the deal, albeit at the lower end of a 417p to 426.5p price range.
Shares in Merlin, which also owns attractions such as Madame Tussauds and Alton Towers, closed down 2.41 per cent at 416.2p.
Blackstone and CVC floated the theme park owner in November 2013 for £3.4bn and has since been selling down its stake in the group.
Last week, Merlin said revenues rose five per cent to £1.25bn for the full year while pre-tax profits increased 35 per cent to £249m.