Directive (EU) 2019/1937 of the European parliament and of the Council of 23 October 2019 on the protection of persons who report breaches of Union law prohibits retaliation against whistleblowers, particularly in the form of coercion, intimidation, discrimination, unfavorable or unjust treatment. This potential of relation to EU anti- discrimination legislation is not entirely clear. The current limited judicial practice from the Czech Republic still lacks clear answers. The aim of this paper is to assess and analyze the relationship between EU legislation on whistleblower protection and anti-discrimination legislation.