Let's say your data are in A2:A100 and in C2:C50.
Select the first range A2:A100.
A2 should be the active cell in the selection.
On the Home tab of the ribbon, click Conditional Formatting > New Rule...
Select 'Use a formula to determine which cells to format'.
Enter the formula
=COUNTIF($C$2:$C$50, $A2)
Click Format...
Activate the Fill tab.
Select a highlight color.
Click OK, then click OK again.
Next, select the other range C2:C50.
C2 should be the active cell in the selection.
Follow the same steps as for the first range, but with the formula
=COUNTIF($A$2:$A$100, $C2)