The lack of obvious morphological differences limits species identification in many marine planktonic copepods. Morphological identification is very time-consuming and depends on prior taxonomic training. Consequently, molecular methods are increasingly used to support taxonomic approaches. Copepod species are often widespread and can occur in very high abundances. Only few diagnostic characters are used for identification in quantitative analysis and species may be overlooked. Thus, it is not surprising that increasing evidence for cryptic and pseudocryptic speciation is found within copepods. Morphological identification often requires looking at minute details of antennules and other body parts and preparing specimens for morphological analysis may prevent molecular approaches. Especially in small sized genera (less than 1 mm), the entire organism is needed for molecular approaches to yield enough DNA. We present an integrative approach that uses the same individual for both morphological and molecular analysis (i.e. next generation sequencing). Non-destructive DNA extraction is performed to retrieve the copepod exoskeleton for morphological taxonomic analysis. The method will be applied to small-sized copepod genera (e.g. <em>Paracalanus </em>, <em>Microcalanus </em>) that occur across several climate zones. The usability of the method for morphological analysis will be discussed. Finally, the phylogeography of each genus will be compared to the results of the other genera.