Environmental DNA metabarcoding is a powerful molecular tool for noninvasively surveying species richness in ecosystems. This review summarizes the use of eDNA metabarcoding for animal and plant community surveys, challenges in estimating relative abundance, and applications in ecology, conservation, and biomonitoring. It highlights the potential of eDNA metabarcoding to complement conventional methods, particularly in freshwater, marine, and terrestrial environments. The review discusses the spatial and temporal scales of eDNA information, guidelines for study design, and the importance of bioinformatic filtering and transparency. It also addresses challenges in the field, laboratory, and data analysis, including primer bias, library preparation, and the need for standardized protocols. The review emphasizes the importance of understanding the origin, state, and fate of eDNA to improve accuracy in abundance estimation. It also discusses the use of eDNA in various ecosystems, including groundwater, sediment cores, and airborne samples, and the need for further research to determine the scale of inference for different sample types. The review concludes with recommendations for improving the accuracy and reliability of eDNA metabarcoding, including the use of standardized protocols, quality assurance steps, and the integration of eDNA with other data types for more comprehensive biodiversity assessments.Environmental DNA metabarcoding is a powerful molecular tool for noninvasively surveying species richness in ecosystems. This review summarizes the use of eDNA metabarcoding for animal and plant community surveys, challenges in estimating relative abundance, and applications in ecology, conservation, and biomonitoring. It highlights the potential of eDNA metabarcoding to complement conventional methods, particularly in freshwater, marine, and terrestrial environments. The review discusses the spatial and temporal scales of eDNA information, guidelines for study design, and the importance of bioinformatic filtering and transparency. It also addresses challenges in the field, laboratory, and data analysis, including primer bias, library preparation, and the need for standardized protocols. The review emphasizes the importance of understanding the origin, state, and fate of eDNA to improve accuracy in abundance estimation. It also discusses the use of eDNA in various ecosystems, including groundwater, sediment cores, and airborne samples, and the need for further research to determine the scale of inference for different sample types. The review concludes with recommendations for improving the accuracy and reliability of eDNA metabarcoding, including the use of standardized protocols, quality assurance steps, and the integration of eDNA with other data types for more comprehensive biodiversity assessments.