Within the Biodiversity Genomics Europe project, the "Pollinator Communities" case study was designed to evaluate pollinator diversity in urban gardens in comparison with agricultural fields, to understand the role of urban habitats for pollinator conservation. This SOP describes the sampling design and Malaise trap fieldwork to retrieve pollinator bulk samples for metabarcoding analysis. This case study involved paired sampling, choosing one large garden and one agricultural field with no more than 20 Km distance between them, to perform a parallel sampling using a Malaise trap per site. Tubes with specimens of both traps were collected on the same day of the week, during five weeks. The "Biodiversity Genomics Europe | Pollinator Communities – Malaise trap sampling” intends establishing a baseline of pollinator (and other arthropods) monitoring along habitats that function as surrogates for ecosystem services.