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From Citizendium, the Citizens' Compendium

Naturalism can mean a variety of different things, but mostly it refers to philosophical positions which hold that "nature is all that is", and can be contrasted with supernaturalism. There are many other uses of the word naturalism though.

Metaphysical v. methodological naturalism

In recent discussions over science education, specifically over the teaching of evolution and intelligent design, much has been made over the question of whether science is "naturalistic" or not. This has led philosophers like Barbara Forrest to draw a distinction between 'methodological' and 'metaphysical' or 'philosophical' naturalism - the former being a component of the method of the natural science, while the latter being optional and substitutable with, say, theism or some form of supernaturalism^[1].

References

1. ↑ Barbara Forrest, Methodological Naturalism and Philosophical Naturalism: Clarifying the Connection, Internet Infidels