'microfauna' originates from a modern compound of Greek and Latin elements: the Greek prefix 'micro-' from 'mikros' meaning 'small' plus the Latin-derived 'fauna' meaning 'animals (collectively)'.

'microfauna' developed as a scientific compound in English (often written earlier as 'micro-fauna') in the late 19th to early 20th century to refer specifically to very small animals; the hyphenated form 'micro-fauna' gradually gave way to the closed form 'microfauna'.

Initially formed to mean 'small animals' in a scientific context, its meaning has remained largely stable and continues to denote collectively the microscopic animals of an environment.