This paper presents a novel scheme for the annotation of hate speech in corpora of Web 2.0 commentary. The proposed scheme is motivated by the critical analysis of posts made in reaction to news reports on the Mediterranean migration crisis and LGBTIQ+ matters in Malta, which was conducted under the auspices of the EU-funded C.O.N.T.A.C.T. project. Based on the realisation that hate speech is not a clear-cut category to begin with, appears to belong to a continuum of discriminatory discourse and is often realised through the use of indirect linguistic means, it is argued that annotation schemes for its detection should refrain from directly including the label ‘hate speech,’ as different annotators might have different thresholds as to what constitutes hate speech and what not. In view of this, we propose a multi-layer annotation scheme, which is pilot-tested against a binary ±hate speech classification and appears to yield higher inter-annotator agreement. Motivating the postulation of our scheme, we then present the MaNeCo corpus on which it will eventually be used; a substantial corpus of on-line newspaper comments spanning 10 years.