Entry 4 senses · 2 variants Webster, 1913 Emarginate · E·mar·gi·nate · IPA v. t. a. 01 v. t. To take away the margin of. 1. To take away the margin of. 02 a. Having the margin interrupted by a notch or shallow sinus. 1. Having the margin interrupted by a notch or shallow sinus. 2. Notched at the summit.(Bot.) 3. Having the edges truncated.(Cryst.)