Yes, in order to run VM's in different VLANs, configure the port as a trunk port (for Cisco), or tagged port (for other switches).
see Sample configuration of virtual switch VLAN tagging (VST Mode) (1004074) | VMware KB
When you configure the virtual port groups, make sure that in case you are also going to create one for the physical switch port's native/default VLAN, that you don't assign the VLAN-ID on this port group.
André