The Bibby Line Group, which handles distribution for Nisa-Today's, has become the majority shareholder in Costcutter.
The Liverpool-based logistics group has acquired a 51% shareholding in the company, which includes the stake previously held by Icelandic bank Kaupthing.
Costcutter said that the existing management team under executive chairman Colin Graves would continue and would be joined on the board by three non-executives from Bibby Line Group.
The deal further cements the inter-dependence between Costcutter and Nisa-Today's. The two groups abandoned a controversial merger proposal last year.
Neil Turton, chief executive officer of Nisa-Today's, said: "Bibby Group and Costcutter Supermarkets are long-term partners of Nisa-Today's (22 and 20 years respectively) and both have long-term contracts with us."
Costcutter retailer Richard Terrell said retailers had been informed and assured that it would not affect their businesses. "It's business as usual, that's what we're hearing from the sales team," he told C-Store.

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