Abstract : Accurate recognition of airborne pollen taxa is crucial for understanding and treating allergic diseases, which affect an important proportion of the world population. Modern computer vision techniques enables the detection of discriminant characteristics. Apertures is one of these characteristic that has been little explored up to now. In this paper, a flexible method of detection, localization and counting of apertures of different pollen taxa with varying appearances is proposed. Apertures are described based by primitive images following the Bag-of-Words strat-egy. A confidence map is estimated based on the classification of sampled regions. The method is designed to be extended modularly to new aper-ture types employing the same algorithm by building individual classi-fiers. The method was evaluation on the top 5 allergenic pollen taxa in Germany and robustness to unseen particles was verified.