Step 1: Recall the three-domain classification.
The three-domain system of classification proposed by Carl Woese is based on the comparison of
\[
\boxed{\text{16S rRNA sequences}.}
\]
These sequences serve as molecular markers for determining evolutionary relationships among organisms.
Step 2: Choose the correct option.
Hence,
\[
\boxed{\text{16S rRNA}}
\]
is the molecular marker used in the creation of the three domains.
Therefore, the correct option is \(\boxed{(C)}\).