Multispectral Imaging Flow Cytometry (MIFC) using the Imagestream X MkII instrument was currently introduced for pollen analysis of recent and fossil pollen. The method allows processing up to 2000 objects/s by simultaneously taking up to 12 microscopic images per object. Based on the images, multispectral patterns, scatter information, and morphological parameters of the pollen can be easily and accurately accessed in high throughput. This enables a powerful way of upscaling pollen analysis and pollen phenotyping to sample amounts, rarely feasible to be processed by classical microscopy, while at the same time providing accurate pollen trait measurements based on hundreds to thousands of processed pollen images. In addition, pollen images can be used for automated pollen identification via machine learning techniques such as Convolutional Neural Networks (CNNs).