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The species P. cubaensis, P. alayoi, P. macromischoides, P. naylae, and the P. cubaensis jr. syn. P. grayi Mann (an unresolved jr. homonym) are either one highly variable species or a complex of cryptic species. Each name is based on one or very few collections. New material collected in 2012 by R. S. Anderson does not fall neatly into existing categories. Any identifications to these species should be considered suspect until more is known about species boundaries. Pheidole bakeri might be part of this complex too.
| Scientific Name | Status | Publication | Pages | ModsID | GoogleMaps |
| Pheidole cubaensis | n. sp. | Mayr, G., 1862, Myrmecologische Studien., Verhandlungen der Zoologisch-Botanischen Gesellschaft in Wien 12, pp. 649-776: 747-748, (download) | 747-748 | 4445 | |
| Pheidole cubaensis | Wilson, E. O., 2003, Pheidole in the New World. A dominant, hyperdiverse ant genus., Cambridge, MA: Harvard University Press: 624, (download) | 624 | 20017 |
Type specimens: Lectotype Pheidole cubaensis: casent0601285; Paralectotype Pheidole cubaensis: casent0601286; paratype Pheidole macromischoides: jtlc000016444