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Biodiversity indices are used by scientists to measure and monitor biodiversity within an ecosystem, and to communicate information about the ecosystem and about the impact of human activities. Nowadays, biodiversity indices are an important component within the assessment of ecosystems, a high-level objective for marine policy (e.g. Marine Strategy Framework Directive, UN Convention on Biological Biodiversity). However, diversity is not always considered in the assessment algorithms or they are used in various forms, which makes it difficult to compare between diversity assessment results. In this contribution, we illustrate the pros and cons of using different biodiversity indices in assessments based on the EU benthic indicator work. The Devotool, MARMONI and WISER databases show that a large set of indicators have been defined for assessing the structural and functional aspects of the benthic ecosystem. Forty-six benthic indicators were listed, of which 48% consider a biodiversity aspect. Those indicators consist of different algorithm types (mainly direct measurements or single, multi-metric and multivariate types). In the benthic indicators, biodiversity is usually assessed as number of species and/or Shannon diversity. In cases where biodiversity shows no relationship or a unimodal relationship with a pressure, biodiversity indices are usually not included in the ecosystem assessment. Consequently, the question arises whether diversity is really a good indicator for evaluating status and for detecting impacts of human pressures. Diversity usually shows a relationship with a pressure (Pearson & Rosenberg, 1978), but the literature, EU indicator intercalibration reports and own studies (De Backer et al., 2014) showed that this relationship is not always straightforward. In Belgian studies on the effects of sand extraction, dredge disposal and offshore wind energy exploitation, the diversity response to these pressures varied. In some coastal areas in the Mediterranean region, the biodiversity did not respond to existing pressures. On the other hand, the pressure-response relation between a chemical pollutant gradient and benthic indicators in the North Atlantic was quite clear. So, responses are case specific, and differ depending on study area, data type, but also on the diversity index used . Diversity indices based on Number of Species show a more direct and rapid response to different pressures than others (e.g. Simpson index). This difference in response, however, should not hamper a consistent ecosystem assessment. If diversity indices are included, an adequate definition of the assessment settings (e.g. data, pressure window, index boundaries) suffices to ensure a reliable and comparable assessment. The use of diversity as an indicator in ecosystem assessments is under debate, but also appears to be necessary. Hence, an appropriate benthic biodiversity index should be selected for each assessment, taking into account the strengths and weaknesses of each index.