Yes, you need to trunk the port(s) connecting to your ESX server. If the sane 3560 is serving as a router for you, then you also need to create an SVI with an IP address:
Example
layer-3 vlan (SVI)
interface vlan 10
ip address 10.10.10.1 255.255.255.0
layer-2 vlan
vlan 10
name ESX server vlan
add the port(s) to vlan 10 and trunk it
HTH