[5] P. pygmaea was initially reported as being endemic to Malabon, Metro Manila in the Philippines, where found at shady river banks.

[3][5] The species has now been extirpated from this area as it was reclaimed, leading to its status as critically endangered by the IUCN.

[1] More recently, it has been discovered at a range of other locations in Southeast Asia, including Culion Island, Bali, Sulawesi and Singapore.

[3] P. pygmaea lives in shallow, tropical brackish water and mangrove areas where mainly found on muddy bottoms or among plants.

[1][3] A colorless and nearly transparent species, the dwarf pygmy goby has a moderately elongated and robust body.

The posterior angle of the maxillary extends beneath the anterior part of the eye, up to the middle of pupil.