The blackfin stonefish was first formally described in 1875 by the British zoologist Francis Day with the type locality given as Kurachi in Sind, modern Karachi in Pakistan.

[3] The genus name combines pseudo meaning "false" with Synanceia, this species being considered by Day to be similar to Leptosynanceia, except for its vomerine teeth.

The specific name melanostigma means "black-spotted", presumed to be an allusion to the black spots on the body and fins.

The anal, pelvic and pectoral fins have yellow bases and wide black distal bands.

[7] The blackfin stonefish is found in the northwestern Indian Ocean but its actual distribution is not well known.