Board Thread:Questions and Answers/@comment-5757968-20150613205142/@comment-4651179-20150613210302

The second logo has not been used in Earth-616 (at least very often as far as I know).

The first logo is the classic S.H.I.E.L.D. logo, while the second one was created for Ultimate S.H.I.E.L.D.

The only difference would be that the second logo is a minimalistic version of the classic logo.