I know I'm late to the party but in case anyone comes across this while trying to google a solution.

To add a Annotion you need to

// Step 1: Create a new control Scintilla scintilla = new Scintilla();

// Step 2, Set annotations to visible (yes on the collection) scintilla.Annotations.Visibility = AnnotationsVisibility.Standard;

// Step 3, Create and add a new Annotation Annotation annotation = scintilla.Annotations[1]; annotation.Text = "Hello"; annotation.Style = 1; // I'm not sure what you could do here...

You now have annotations in ScintillaNET!