Anales del Jardín Botánico de Madrid is indexed in: Web of Science: Journal Citation Reports (JCR), Science Citation Index Expanded (SCI), Current Contents - Agriculture, Biology & Environmental Sciences and BIOSIS Previews; SCOPUS, CWTS Leiden Ranking (Journal indicators) Core publication, Agricola, Agris, Aquatic Science & Fisheries Abstracts, Biosis Toxicology, Biological Abstracts, Cab Abstracts, Csa Life Sciences, Global Health, REDIB, DOAJ, Pascal, Dialnet,  Sherpa Romeo and ÍnDICEs CSIC. It is indexed in Latindex Catalogue 2.0 and has obtained the FECYT Seal of Quality.

The Journal provides information about new species for inclusion in the databases TROPICOS (Vascular Plants, Bryophyte), International Plant Name Index and IndexFungorum.