In order to analyze the status of web domain certificates in the Web PKI, a relevant set of X.509 certificates must be built. This dataset was created based on the Alexa Top 1 Million (Top1M) List (available on 26 August 2021) and the Majestic Top 1 Million List (available on 21 November 2022) containing the most visited websites. We collected the X.509 certificates for the web domains in the Alexa Top1M list (file "ListAlexaFinal.txt") with two dedicated scripts in the dataset, namely "ScriptCollectCertificates.sh" and "StartScript_CollectCertificates.sh".