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Supplementary Information: The online version contains supplementary material available at https://doi.org/ 10.1038/s41598-021-95996-3., Sequence data for UE2298/MS060 can be downloaded from the European Nucleotide Archive (accession number: PRJEB47085). Newly reported present-day mtDNA sequences are deposited into GenBank (MZ920249 - MZ921390). Additional requests should be addressed to: marina.silva@crick.ac.uk; gonzalo.oteo-garcia@hud. ac.uk; m.b.richards@hud.ac.uk., Historical records document medieval immigration from North Africa to Iberia to create Islamic al-Andalus. Here, we present a low-coverage genome of an eleventh century CE man buried in an Islamic necropolis in Segorbe, near Valencia, Spain. Uniparental lineages indicate North African ancestry, but at the autosomal level he displays a mosaic of North African and European-like ancestries, distinct from any present-day population. Altogether, the genome-wide evidence, stable isotope results and the age of the burial indicate that his ancestry was ultimately a result of admixture between recently arrived Amazigh people (Berbers) and the population inhabiting the Peninsula prior to the Islamic conquest. We detect differences between our sample and a previously published group of contemporary individuals from Valencia, exemplifying how detailed, small-scale aDNA studies can illuminate fine-grained regional and temporal differences. His genome demonstrates how ancient DNA studies can capture portraits of past genetic variation that have been erased by later demographic shifts-in this case, most likely the seventeenth century CE expulsion of formerly Islamic communities as tolerance dissipated following the Reconquista by the Catholic kingdoms of the north., We thank the Museo Municipal de Arqueologia y Etnologia de Segorbe for granting access to their collections and the Conselleria d'Educacio, Investigacio, Cultura i Esport de la Generalitat Valenciana for granting the permissions for the study. We thank Lara Cassidy, Valeria Mattiangeli and Dan Bradley for valuable advice and technical support. Part of this work was delivered via the BBSRC National Capability in Genomics and Single Cell Analysis (BBS/E/T/000PR9816) at Earlham Institute by members of the Genomics Pipelines and Core Bioinformatics Groups. We wish to acknowledge the use of the Orion High Performance Computing cluster at the School of Applied Sciences, University of Huddersfield. M.S., G.O.G., A.Fi., P.J., M.G.B.F., K.D., B.Y. were supported by a Leverhulme Doctoral Scholarship awarded to M.B.R. and M.P. P.S., M.B.R., and M.P. acknowledge FCT (Fundacao para a Ciencia e a Tecnologia) support through project PTDC/EPH-ARQ/4164/2014, partially funded by FEDER funds (COMPETE 2020 project 016899). P.S., A.Br., A.R. and T.R. acknowledge FCT support through project PTDC/SOC-ANT/30316/2017. P.S. acknowledges the "Contrato-Programa" UIDB/04050/2020 and contract CEECINST/0007772018 funded by FCT I.P. A.A., A.O., and A.T. acknowledge the support of the Italian Ministry of Education, University and Research for the projects "Dipartimenti di Eccellenza" Program (2018-2022) -Department of Biology and Biotechnology "L. Spallanzani," University of Pavia and PRIN2017 20174BTC4R. The KORA research platform (KORA, Cooperative Research in the Region of Augsburg) was initiated and financed by the Helmholtz Zentrum Munchen -German Research Center for Environmental Health, which is funded by the German Federal Ministry of Education and Research and by the State of Bavaria. Furthermore, KORA research was supported within the Munich Center of Health Sciences (MC Health), LudwigMaximilians-Universitat, as part of LMUinnovativ.