The visits comes after both governments having signed significant agreements.
Marles describes his trip to Vanuatu trip as part of "working together as a Pacific family on shared Pacific priorities".
The visit will include discussions on both Efate and Santo with provincial leaders.
Marles, who is also Australia's Defence Minister, will also present a new patrol boat to the Vanuatu Police Force.
In December both governments signed a bilateral security agreement which would provide strengthened cooperation on defence, border security and humanitarian assistance.