The NEBC herbarium limits its scope to the six New England states and is the largest collection for this region anywhere. The vascular herbarium (with more than 253,000 sheets) is currently being integrated with the vascular holdings of the Harvard University Herbaria, but will be maintained in separate color-coded folders (along with Harvard's specimens from the New England states). The Club's nonvascular herbarium is also in the process of being recurated and integrated into Harvard's Farlow Herbarium. The collection can be searched on the specimen database.

All loans of specimens are handled through the Harvard University Herbaria. The Club's holdings include many specimens collected by Merritt Fernald, Kate Furbish, James Watson Robbins and William Oakes. The vascular herbarium has particularly good representation for Mt. Desert Island, Maine; Coos Co., New Hampshire; the vicinity of Boston, Massachusetts; Essex Co., Massachusetts; Cape Cod; Nantucket and Martha's Vineyard, Massachusetts. Type specimen data for vascular plants are included in the Harvard University Herbaria computer database of vascular type specimens.

The Atlas of the Flora of New England is a web based project by Ray Angelo and David Boufford to map New England flora based on specimens in the major herbaria of Maine, New Hampshire, Vermont, Massachusetts, Rhode Island and Connecticut, with primary emphasis on the holdings of the New England Botanical Club herbarium (NEBC).

NOTE: The server hosting the Atlas of the Flora of New England will be taken offline indefinitely on April 30, 2008. Status updates will be posted at http://www.ray-a.com.