Ferdinand and Isabellas Inquisition?
Unfortunately, it started long before F and I, and lasted long after they were gone.
http://www.jewishvirtuallibrary.org/jsource/Judaism/Marranos.html
http://en.wikipedia.org/wiki/Morisco
Dhimmis in Muslims lands were not exactly safe and protected, but they were first-class citizens by comparison to Jew, Muslims, converts from these religions to Catholicism, or their descendants in Iberia.