Melissopalynological studies are useful to determine the floral contents and geographical origin of honey samples. The great botanical diversity in the Amazon allows bees to produce honey that is highly valuable in Peruvian culture. However, pollen analyses and labels that provide information on honey contents are scarce; therefore, people do not know what types of honey they are consuming and paying for, especially when many Amazonian honeys are traditionally referred to as being monofloral honey types with medicinal properties. For this reason, we conducted a melissopalynological study to evaluate the pollen content of 14 honey samples from lowland and highland regions of the Peruvian Amazon. A total of 40 pollen types from 28 families were identified and most of the samples were multifloral. Pollen from Fabaceae, Asteraceae and Citrus were very frequent in the samples while Myrciaria dubia, Trema and Paullinia were frequently found in the samples. Pollen from Bombax, Gouania and Mimosa were infrequent within the samples. Pollen concentration class values per 10 g of honey varied from very rich to very poor and a low index of similarity in pollen content was observed between the samples, but there was a higher similarity between samples that came from the same region. Most of the identified floral sources in the honey are related to taxa that are traditionally used for medicinal purposes. The bioactive compounds of the nectar of these plants may be producing the ‘healthier’ properties that people associate with Amazonian honeys in Peru. This pollen study provides important information on the floral source preferences of bees and on honey contents, which can be used by traditional beekeepers and the public in general. Melissopalynological analyses are also useful for promoting the production and consumption of high-quality local honeys from the Peruvian Amazon.