Large collections of historical biodiversity expeditions are housed in natural history museums throughout the world. Potentially they can serve as rich sources of data for cultural historical and biodiversity research. However, they exist as only partially catalogued specimen repositories and images of unstructured, non-standardised, hand-written text and drawings. Although many archival collections have been digitised, disclosing their content is challenging. They refer to historical place names and outdated taxonomic classifications and are written in multiple languages. Efforts to transcribe the hand-written text can make the content accessible, but semantically describing and interlinking the content would further facilitate research. We propose a semantic model that serves to structure the named entities in natural history archival collections. In addition, we present an approach for the semantic annotation of these collections whilst documenting their provenance. This approach serves as an initial step for an adaptive learning approach for semi-automated extraction of named entities from natural history archival collections. The applicability of the semantic model and the annotation approach is demonstrated using image scans from a collection of 8, 000 field book pages gathered by the Committee for Natural History of the Netherlands Indies between 1820 and 1850, and evaluated together with domain experts from the field of natural and cultural history.