Harmful dinoflagellate cysts (e.g. dinocysts) represent a great threat to marine and coastal ecosystems and even human health. As dinocysts have resistant cell walls that allow dinoflagellate species to successfully survive harsh environments, they can easily pass through multiple barriers during biological invasions and successfully colonize new locations. In introduced ranges, dinocysts often serve as seeds for harmful algal blooms, which can result in large-scale environmental disasters and economic losses. Correct identification of dinocysts represents the first step for both ecological studies and management programs. However, traditional methods, which are based on morphological observations, pose great technical challenges for dinocysts. Recent advances in molecular techniques, such as high-throughput sequencing-based metabarcoding, have tremendously revolutionized our abilities to detect marine biodiversity. Here, we summarize species composition of non-indigenous/cryptogenic dinocysts and their identification methods commonly used in China, discuss major problems in traditional morphological identification and technical issues of molecular identification, and finally propose future perspectives for the efficient identification of non-indigenous dinocysts using high-throughput sequencing-based metabarcoding. We also discuss technical issues that should be addressed before high-throughput sequencing-based metabarcoding can be widely used for dinocyst identification at large geographical scales.

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