Samir S. answered 02/24/21
Experienced ACT/SAT Language/Reading tutor
This is a complex question.
Certainly Europeans noticed the differences in physical appearance between themselves and the native peoples they encountered, but it is important to remember that racism as the concept we know today is a relatively recent notion, with its roots in 19th and 20th century racial theory.
Far more important to the European colonizers were the cultural, philosophical, and religious differences they perceived between themselves and the Native Americans. It is also important to differentiate between the various groups of European explorers and colonists as their encounters with Native peoples run the gamut from friendly to genocidal.
For example, in the early 16th Century, the French fur traders to what is now modern day Quebec were far more interested in maintaining good relationships with the local Indigenous peoples than they were in establishing a permanent colony. It was good business for them to cultivate friendly relationships with Indigenous peoples, and there are many records of intermarriage and co-existence between the French and the Indigenous nations. This can be contrasted with Spain's far more aggressive, conquest-based forays into Florida and Central America. Spain's conquest was spurred on and justified by the Catholic Church, leading to far more warfare and the decimation of many Indigenous peoples.