Some journals are located in the two data bases and some are located in one without the other. So what is the difference and which one is more distinguished or superior to the other?
Be very careful in this matter. People used to talk about ISI indexed journals. However, when one talks about this be aware that: International Scientific Indexing (ISI) is a bogus impact factor: https://isindexing.com/isi/index.php (is a notorious example of a misleading metric https://beallslist.net/misleading-metrics/).
It is misleadingly referring to the Institute for Scientific Information (ISI) that used to provide indexing of major international journals and often referred to as ISI impact factor. It is nowadays the well-known Science Citation Index (SCIE) that is provided by Clarivate. The journals that are really indexed in WoS database/indexing can be found here https://mjl.clarivate.com/home (either in ESCI or SCIE/SSCI) or in the enclosed file, all property of Clarivate (the successor of Thomson Reuters).
Bedir Yosif back to your question:
-Clarivate is having the most stringent criteria (https://clarivate.com/webofsciencegroup/journal-evaluation-process-and-selection-criteria/). They suppress (a limited number of) titles only once a year (https://jcr.help.clarivate.com/Content/title-suppressions.htm).
-They use a ‘filter’ index, journals (potentially) eligible for an impact factor are indexed in their ESCI.
-Scopus (https://www.scopus.com/sources.uri?zone=TopNavBar&origin=searchbasic) index journals with CiteScore. They use a lower number of criteria compared to Clarivate (https://www.elsevier.com/solutions/scopus/how-scopus-works/content/content-policy-and-selection)
-Roughly 3-4 times a year they publish an updated list of discontinued titles for titles with ‘issues’
Because of the differences in inclusion criteria you sometimes find a journal in Scopus and not in Clarivate's SCIE and vice versa.
Scopus is the largest database that publishes articles, abstracts and scientific citations. This database has four categories to arrange articles. You can view them here. To learn more about Scopus magazines, you can review this article. As for ISI, it is an old institution founded by Eugene Garfield in 1956 AD to index articles, citations and scientific documents in general and the publishing standards in these journals are not easy at all because of the strict criteria they take to accept articles. To learn more about ISI journals, you can click here. Without any exaggeration, ISI articles are the most important articles available in the world and in the second place comes Scopus, in any case, Scopus contains most of the articles registered in ISI in addition to a large number of other articles, and this indicates that the chance of being published in Scopus is higher than the opportunity to be published in ISI.