Schistometopum thomense is a species of amphibian in the family Dermophiidae, endemic to São Tomé and Ilhéu das Rolas.

[5] The species has been described under the following synonyms:[2] Interfamilial and intergeneric relationships of the São Tomé caecilian are well supported by analyses of mitochondrial (mtDNA) sequence data.

[6] Within Schistometopum, Wilkinson et al. (2003) found that S. thomense is sister to S. gregorii (an East African species distributed in Kenya and Tanzania) which was also determined to be its lone congener.

[8] However, species-level phylogenetic relationships of S. thomense have yet to be fully determined, given the recent discovery of Schistometopum ephele, a cryptic species on São Tomé Island.

Zooming out to higher-level phylogenetic relationships, S. thomense was historically placed in the Caeciliidae,[6][8][11][12] a highly unresolved grouping that was paraphyletic with respect to the Typhlonectidae and the Scolecomorphidae.