The general appearance of Hoburogekko resembles that of the living species Agamura persica, Bunopus tuberculatus, Pristurus carteri, Ptenopus carpi, and Teratoscincus przewalskii, all of which have blunt and tall snouts.

[3] The large size of the jugal bone suggests that it may have extended backward to form a postorbital bar, in which case Hoburogekko would appear more primitive.

[1] However, a paucity of distinguishing characteristics in the two known specimens of Hoburogekko meant that its evolutionary relationships were not evaluated in a phylogenetic analysis until many years after its first description.

The phylogenetic analysis of Daza et al. (2012) found Hoburogekko to be closely related to the living species Phyllurus platurus, commonly called the broad-tailed gecko.

In the analysis, Hoburogekko and Phyllurus are more closely related to the legless pygopodids than they are to most other geckos, burt this position need to be re-evaluated, including more members of the crown group Gekkota.