How to delete an annotation in Evince?

That is because at the moment you can not remove them. Developers are planning this feature for future releases.

Right-click annotation icon, “Remove annotation”

Simply right click an annotation and select “Remove annotation” from the context menu. I have Evince 3.14 according to the Evince bug tracker the issue was solved summer 2014

Below is a hack for older Evince versions.

There is a hack for the determined.

Open the pdf in a simple text editor (it should not try to “fix” it). I used nano.

Scroll all the way to the bottom (hold Page Down).

The annotations are in a non-binary format (thus relatively readable) at the very end of the PDF. In a PDF with two annotations the final part looks like this:

%%EOF
4 0 obj <</Type /Page /Contents 5 0 R /Resources 3 0 R /MediaBox [0 0 595.276 841.89 ] /Parent 15 0 R /Annots 67 0 R >> endobj
65 0 obj <</Type /Annot /Rect [179.8028910464 509.6564724919 203.8028910464 533.6564724919 ] /Subtype /Text /M (D:20141219111205) /C [1 1 0 ] /Popup 66 0 R /T (\FE\FF\00N\00a\00m\00e\00 \00o\00f\00 \00a\00u\00t\00h\00o\00r) /P 4 0 R /Contents (\FE\FF\00T\00h\00i\00s\00 \00i\00s\00 \00a\00 \00t\00e\00s\00t\00 \00a\00n\00n\00o\00t\00a\00t\00i\00o\00n\00 \00I\00 \00h\00a\00v\00e\00 \00n\00a\00m\00e\00d\00 \00i\00t\00 \00n\00u\00m\00b\00e\00r\00 \001\00.) >> endobj
66 0 obj <</Type /Annot /Rect [203.8028910464 359.6564724919 403.8028910464 509.6564724919 ] /Subtype /Popup /M (D:20141219111148) /Parent 65 0 R >> endobj
67 0 obj [65 0 R 68 0 R ] endobj
68 0 obj <</Type /Annot /Rect [385.2919093851 365.8141596548 409.2919093851 389.8141596548 ] /Subtype /Text /M (D:20141219111217) /C [1 1 0 ] /Popup 69 0 R /T (\FE\FF\00N\00a\00m\00e\00 \00o\00f\00 \00a\00u\00t\00h\00o\00r) /P 4 0 R /Contents (\FE\FF\00T\00h\00i\00s\00 \00i\00s\00 \00a\00 \00t\00e\00s\00t\00 \00a\00n\00n\00o\00t\00a\00t\00i\00o\00n\00:\00 \00I\00 \00h\00a\00v\00e\00 \00n\00a\00m\00e\00d\00 \00i\00t\00 \00n\00u\00m\00b\00e\00r\00 \002\00.) >> endobj
69 0 obj <</Type /Annot /Rect [409.2919093851 215.8141596548 609.2919093851 365.8141596548 ] /Subtype /Popup /M (D:20141219111206) /Parent 68 0 R >> endobj
xref
0 1
0000000001 65535 f
4 1
0000162703 00000 n
65 5
0000162831 00000 n
0000163168 00000 n
0000163325 00000 n
0000163359 00000 n
0000163698 00000 n
trailer
<</Size 70 /ID [(J]\C3\F8\A9ApV\92\B7\96\AB\A6\B2) (\FDWڸG\BA'8\)\E4\CE\B7) ] /Root 63 0 R /Prev 161245 /Info 64 0 R >> 
startxref
163855
%%EOF
<----HERE IS THE ACTUAL END OF FILE (note this was added by me, not part of the PDF)

I managed to delete specific annotations by removing the correct lines, but it may take some trial and error. Always create a backup before you start messing with this.

When you remove a line, you must also remove all lines that reference it with a /Parent The number references the number at the start of the line you removed.

NOTE: The part after the upper %%EOF can be removed entirely to remove all annotations. This seems fairly safe.

This works for me:

gvfs-set-attribute /path/to/file.pdf metadata::evince::bookmarks ''

(evince 3.4.0, Ubuntu 12.04)