Molecular analysis of the DNA sequences of the internal transcribed spacer (IT) region of S. thailandica showed that the species was part of the Boletineae, one of several lineages of Boletales recognized taxonomically at the level of suborder.
The similarity between S. thailandica and S. squarepantsii was confirmed with molecular analysis, which showed a 98% match between large subunit ribosomal DNA sequences of the two—a value typical of many species in the same genus of Boletaceae.
Spongiforma is sister (sharing a common ancestor) to the genus Porphyrellus; Spongiforma and Porphyrellus form a clade that is sister to Strobilomyces.
All three genera are members of the family Boletaceae.

The phylogenetic relationships determined by molecular techniques are not consistent with a classification scheme based on similarities in spore morphology.
Several bolete taxa have been proposed to accommodate species with reddish-brown to vinaceous-brown, finely wrinkled (rugulose) to perforated or punctate spores; these include Boletus subgenus Tylopilus, Tylopilus subgenus Porphyrellus, Austroboletus, or Porphyrellus.
Austroboletus tristis and A. longipes, two species from Southeast Asia, share several spore characteristics with Spongiforma thailandica.
 All three species have spores with rugulose surfaces, sometimes with minute punctures, and the spores turn purple in potassium hydroxide.
Additionally, the pores from the three species share similar surface ornamentation visible with scanning electron microscopy.
In contrast to Spongiforma, however, Austroboletus spores do not have an apical pore.
Genetic analysis shows that Spongiforma is more closely allied with the smooth-spored Porphyrellus than with the rugulose-punctate-spored Austroboletus.

Relatively few boletes have an apical pore at the distal end of their basidiospores.
The dark reddish-brown, smooth spores of Porphyrellus amylosporus are truncate with a thin-walled depression.
Some species of Heimioporus have spores with apical pores, but molecular analyses demonstrate that Heimioporus is only distantly related to Spongiforma.

Spongiforma further resembles Austroboletus and Porphyrellus species in the cellular structure of the cap cuticle (pileipellis).
The arrangement, known as a trichodermium, features the outermost hyphae emerging roughly parallel, like hairs, perpendicular to the surface of the fruit body.
The trichodermium comprises chains of short, cylindrical to somewhat moniliform cells (resembling a string of beads) with terminal (end) cells that are cylindrical to club-shaped.
This cellular arrangement is similar to that present in the sterile edges of the tissues that demarcate the locules in Spongiforma.
According to Desjardins and colleagues, this may represent vestiges of what was once cap cuticle or peridial tissue in an ancestor.
Spongiforma is the only genus of the Boletales that forms above-ground fruit bodies that lack a peridium and have many exposed locules lined with basidia that do not forcibly discharge spores.
Molecular analysis of the DNA sequences of the internal transcribed spacer (IT) region of S. thailandica showed that the species was part of the Boletineae, one of several lineages of Boletales recognized taxonomically at the level of suborder. The similarity between S. thailandica and S. squarepantsii was confirmed with molecular analysis, which showed a 98% match between large subunit ribosomal DNA sequences of the two—a value typical of many species in the same genus of Boletaceae. Spongiforma is sister (sharing a common ancestor) to the genus Porphyrellus; Spongiforma and Porphyrellus form a clade that is sister to Strobilomyces. All three genera are members of the family Boletaceae.
The phylogenetic relationships determined by molecular techniques are not consistent with a classification scheme based on similarities in spore morphology. Several bolete taxa have been proposed to accommodate species with reddish-brown to vinaceous-brown, finely wrinkled (rugulose) to perforated or punctate spores; these include Boletus subgenus Tylopilus, Tylopilus subgenus Porphyrellus, Austroboletus, or Porphyrellus. Austroboletus tristis and A. longipes, two species from Southeast Asia, share several spore characteristics with Spongiforma thailandica.  All three species have spores with rugulose surfaces, sometimes with minute punctures, and the spores turn purple in potassium hydroxide. Additionally, the pores from the three species share similar surface ornamentation visible with scanning electron microscopy. In contrast to Spongiforma, however, Austroboletus spores do not have an apical pore. Genetic analysis shows that Spongiforma is more closely allied with the smooth-spored Porphyrellus than with the rugulose-punctate-spored Austroboletus.
Relatively few boletes have an apical pore at the distal end of their basidiospores. The dark reddish-brown, smooth spores of Porphyrellus amylosporus are truncate with a thin-walled depression. Some species of Heimioporus have spores with apical pores, but molecular analyses demonstrate that Heimioporus is only distantly related to Spongiforma.
Spongiforma further resembles Austroboletus and Porphyrellus species in the cellular structure of the cap cuticle (pileipellis). The arrangement, known as a trichodermium, features the outermost hyphae emerging roughly parallel, like hairs, perpendicular to the surface of the fruit body. The trichodermium comprises chains of short, cylindrical to somewhat moniliform cells (resembling a string of beads) with terminal (end) cells that are cylindrical to club-shaped. This cellular arrangement is similar to that present in the sterile edges of the tissues that demarcate the locules in Spongiforma. According to Desjardins and colleagues, this may represent vestiges of what was once cap cuticle or peridial tissue in an ancestor. Spongiforma is the only genus of the Boletales that forms above-ground fruit bodies that lack a peridium and have many exposed locules lined with basidia that do not forcibly discharge spores.
Spongiforma