As nouns the difference between protozoan and ciliates

is that protozoan is any of the diverse group of eukaryotes, of the phylum Protozoa, that are primarily unicellular, existing singly or aggregating into colonies, are usually nonphotosynthetic, and are often classified further into phyla according to their capacity for and means of motility, as by pseudopods, flagella, or cilia while ciliates is plural of ciliate.

As an adjective protozoan

is of, pertaining to, or characteristic of a protozoan.