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Coral reefs are the most biodiverse ecosystems of the ocean and they provide notable ecosystem services. Large-scale monitoring is necessary to understand the effects of anthropogenic threats and environmental change on coral reef habitats and citizen science programs can support this effort. Seventy-two marine taxa found in the Red Sea were surveyed by non-specialist volunteers during their regular recreational dives, using SCUBA Tourism for the Environment (STE) questionnaires. Over a period of 4-years, 7,125 divers completed 17,905 questionnaires (14,487 diving hours). Validation trials were carried out to assess the data reliability (Cronbach’s alpha >50 % in 83.6 % of validation trials), showing that non-specialists performed similarly to conservation volunteer divers on accurate transect. The resulting sightings-based index showed that the biodiversity status did not change significantly within the project time scale, but revealed spatial trends across areas subjected to different protection strategies. Higher biodiversity values were found in Sharm el-Sheikh, within protected Ras Mohammed National Park and Tiran Island, than in the less-regulated Hurghada area. Citizen science programs like STEproject represent novel, reliable, cost-effective models for biodiversity monitoring, which can be sustained and embedded within long-term monitoring programmes, and extended to include a wider geographical scale, while increasing the environmental education of the public.