Species identification is essential to study the impact of environmental changes on community structure and biodiversity in zooplankton. This however, requires high levels of taxonomic expertise, because zooplankton comprises a huge variety of behaviors, forms and life histories in very diverse phyla. Since the advent of molecular methods to identify species it has become evident that morphologically (microscopy) based identification has greatly underestimated species richness and it revealed more complex species biogeographies than previously thought. During the last decade new methods have evolved that allow single species detection and identification (DNA barcoding, proteomic fingerprinting, geometric morphometrics) and multiple species detection in communities (metabarcoding of bulk samples and eDNA, semi-automatic optical identification), which provide different approaches and resulting data. However, bridging the gap between finding species, identifying species and integrating the various methods for a complete understanding of species entities is difficult as the new techniques provide new characters (genetic codes, morphometrics, proteomic spectra, image-based characteristics) that are not easily integrated in species descriptions and studies on community composition. The integration of the various data is however, a prerequisite to ensure the consistency for longterm observational data from microscopy to newer approaches. We will provide an overview over the methodological developments and challenges in zooplankton species identification over the past decades.