Fish, tuna to be precise. This sounds all sorts of wrong, but it really isn't: it's about the control of the economic resources, and tuna was a valuable resource. Since time immemorial, in the South of Spain, there had been (an there still is) a fishing technique called "almadraba" used for fishing tunas. Not all of them were of equal worth, so that is why the Marquess of Cádiz and the Duke of Medina Sidonia fought for the control of the best ones: the almadrabas of Cádiz and the almadrabas of Rota.

This happened in the 15th century, a time when the Crown did not have that much power after civil wars and the Kings giving away far too many possession, and the affairs of the kingdoms were managed by validos (think of them as omnipotent prime ministers).
In 1474, at last, they settled their dispute with the mediation of the Count of Tendilla. The almadrabas of Cádiz were finally given in exclusivity to the Marquis of Cádiz, and those of Rota to the Duke of Medina Sidonia.

To see how vicious the conflict was, I'll quote the peace treaty signed by the Duke and the Marquess, for the terms cannot be any more explicit:

For between us there have been great scandals, discords, and wars, and generally throughout these lands the pillages, and damages, and deaths have grown larger, and, by each of us, have great gatherings of armed men produced raids, deaths, pillages, and devastations...