In accordance with an embodiment, a system and method provides a messaging service in a multitenant application server environment. Deployable resources are usable within the multitenant application server environment and groupings of resources are defined by resource group templates within a domain. One or more partitions are provided, with each partition providing an administrative and runtime subdivision of the domain that can be associated with a tenant. Java message service (JMS) resources are defined within a resource group template or a resource group, and instantiated within a partition from the one or more partitions to enable messaging for applications deployed within the partition and between the one or more partition.