Synchronization of clocks among computing devices in a network includes determining master/slave relations among the computing devices. Some computing devices (e.g., switches) include trunk ports configured to carry traffic for several logical networks; e.g., virtual local area networks, VLANs. A trunk port can be associated with a master/slave setting for each logical network that it is configured for. Synchronization of clocks among the computing devices further includes running a synchronization sequence between a trunk port and each computing device on each of the logical networks configured on the trunk port.