Acknowledgements This work was supported by the European project SEAMoBB: "Solutions for Semi Automated Monitoring of Benthic Biodiversity" funded by ERA-NET MarT-ERA and the Ministry of University and Research (MUR). Anna Thomasdotter was supported by the IMBRSea master program (International Master of Science in Marine Biological Resources), as an Erasmus Mundus Joint Master's Degree (EMJMD) scholarship Awardee. Special thanks to Dr. Kenan O. Matterson for the field sampling and the molecular-related contributions, bioinformatics included. We are grateful to Francesco Paolo Mancuso for his help during the field activity during the first deployment of ARMS. We would like to thank all of the Marine Biology M.Sc. students involved in SEAMoBB project field- and lab-related activities during the 2019 and 2020 campaigns: Giuditta Carbone, Cinzia Cozzulla, Gabriele Giacalone, Alessandro Giordano, Massimiliano Lippi, Giorgia Olivieri, Alberto Orengo, India Ronchi and Alessandra Silvestri. Many thanks to Barbara Mikac for the identification of the Polychaetes in the vagile fauna fraction. Finally, we would like to express our thanks to the diving centers that supported us during the field activities (Rovinj Sub, Rovinj, Croatia; Palinuro Sub, Palinuro, Italy; Accademia Blu Diving Center, Livorno, Italy). We would also like to thank the CIBM, Centro Interuniversitario di Biologia Marina ed Ecologia Applicata "G.Bacci", Livorno, Italy, the Ruđer Bošković Institute, Rovinj, Croatia, and the Hotel Le Tre Caravelle, Palinuro (SA), Italy for their support during the sample processing in the field.

Sequence data and stepwise pipeline outputs associated with the article "Spineless and overlooked: DNA metabarcoding of autonomous reef monitoring structures reveals intra- and interspecific genetic diversity in Mediterranean invertebrates". Preprint available here: 10.22541/au.167085544.47638352/v1 Sequence data is deposited in fastq-format in folders by region (Palinuro.tar.gz, Livorno.tar.gz, and Rovinj.tar.gz) and a separate folder for controls (Controls.tar.gz). Each fastq-file contains sequences for a single PCR replicate named by sample and replicate number. Sample names are described in spineless_sample_names.csv. Positive control sequences are described in SM1_positive_controls.csv. Stepwise pipeline outputs are available in the folder Pipeline_outputs_stepwise.zip Scripts used to generate pipeline outputs as well as other aspects of the final article are available at https://github.com/thomasdotter/spineless-haplotypes.