MongoDB 3.0 : Configure storage engine at collection or database level
You can only use a single storage engine type per mongod instance. There is only a single dbPath setting for a mongod deployment, and you cannot mix &amp; match data files from different storage engines within the same data path.

However, you can use different storage engine configurations within members of a replica set (for example, mmap primary and WiredTiger secondaries). If you do this, you should be wary of differences in performance and be sure to test thoroughly in a QA/staging environment with representative workload.

Another available option is to set storage-engine specific options when creating a collection. For example, you could override the instance-level defaults for WiredTiger and set different options for specific collections (i.e. higher level of compression, or perhaps no compression).