Although it is not generally necessary to indicate that a work appears in a special issue of a journal, you can cite special issues by following the MLA format template. Include the same information you would for an article in a regular issue, adding the special issue’s title, a comma, and the phrase “special issue of” before the journal’s title in the “Title of Container” slot:

Charney, Michael W. “Literary Culture on the Burma-Manipur Frontier in the Eighteenth and Nineteenth Centuries.” Literary Cultures at the Frontiers: Literature and Identity in the Early Modern World, special issue of The Medieval History Journal, edited by Sumit Guha, vol. 14, no. 2, 2011, pp. 159-81.

If a special issue identifies itself not by title but by description (e.g., “special issue on Shakespeare”), include that description and the journal’s title in the “Title of Container” slot:

Frelik, Paweł. “Of Slipstream and Others: SF and Genre Boundary Discourses.” Special issue on slipstream, Science Fiction Studies, vol. 38, no. 1, Mar. 2011, pp. 20-45.