We evaluated the usefulness of herbarium collection databases for assessing patterns of species diversity and distribution based on a dataset from the flowering plant families Moraceae and Myristicaceae from the Peruvian Amazon. For Moraceae, a total of 3523 collections were used representing 134 species. The Myristicaceae were represented by 2113 collections of 46 species. We evaluated the distribution of collections based on 252 grid cells (0.5° size) covering all lowland rainforest in the Peruvian Amazon. We found that collections were concentrated in a few cells and that species diversity clearly increases in relation to collection density. Moraceae were collected in only 45% and Myristicaceae in only 31% of the 252 grid cells. Fifty percent of the collections came from just six and three cells, respectively. Most species were represented by only a small number of collections and collected only in a few grid cells, meaning a few widespread common species tend to dominate the collection records. Not surprisingly, most collections were made close to towns and transport routes. We evaluated the usefulness of rarefaction curves and diversity estimators for comparing diversity between regions. These techniques seem to be of little use for botanical collections due to violations of underlying assumptions. Problems such as accuracy of geographic and taxonomic data and strong bias in the spatial representation of the whole dataset are important to consider when basing conservation analysis, planning, and decision-making on seemingly large databases of biodiversity collections and are discussed in detail.