Melanoconion was originally proposed as a distinct genus by Theobald (1903). The type species, Culex atratus Theobald, 1901, was subsequently designated by Dyar (1905). Dyar & Knab (1906) synonymised Melanoconion with Culex and proposed Mochlostyrax as a distinct genus with caudelli Dyar & Knab, 1906 as its type species. Howard et al. (1915) considered both Melanoconion and Mochlostyrax as synonyms of Culex, and three years later Dyar (1918) recognised them as separate subgenera of Culex. In the same paper, Dyar also proposed Choeroporpa as a subgenus of Culex, with anips Dyar, 1916 as its type species. Choeroporpa included most of the species that Dyar has previously placed in Culex or Mochlostyrax. In a second paper published in the same year, Dyar (1918) proposed Helcoporpa as another subgenus of Culex, with menytes Dyar, 1918 as its type species. Five years later, Dyar (1923) instated Gnophdeomyia Theobald, 1905 as a subgenus (previously synonymised with Culex by ?Brunetti, 1914) and proposed Anoedioporpa as a replacement name for subgenus Isostomyia Coquillett, 1906. Dyar (1928) made significant changes to the classification of New World Culex. He recognised Melanoconion and Mochlostyraxas subgenera and reduced the other nominal generic-level groups to informal sections: Choeroporpa, Helcoporpa and the newly proposed Dinoporpa became sections of Mochlostyrax, and Tinolestes Coquillett, Gnophodeomyia and Anoedioporpa became sections of Melanoconion, which also included americanus (Neveu-Lamaaire) and antillummagnorum Dyar to subgenus Micraedes Coquillett, 1906.Edwards (1932), in his treatment of world Culicidae, reinterpreted the taxonomy of Melanoconion and Mochlostyrax. He considered Melanoconion as a subgenus with Gnophodeomyia, Asebeomyia Aiken, 1911, Tinolestes, Choeroporpa, Helcoporpa and Dinoporpa as its synonyms; restricted subgenus Mochlostyrax to include species included in the Mochlostyrax section of Dyar (1928); synonymised Anoedioporpa with subgenus Isostomyia (currently a valid genus in tribe Sabethini); and transferred americanus and antillummagnorum to subgenus Micraedes. During the same year Komp & Curry (1932) proposed Upsiloporpa as a new subgenus of Culex, with the new species haynei Komp & Curry, 1932 as its type and only included species. Komp (1935) found haynei to be conspecific with menytes, thus Upsiloporpa became another synonym of Melanoconion. Except for the transfer of ocellatus Theobald from subgenus Microculex Theobald to subgenus Melanoconion by Lane & Whitman (1943), Edwards's classification remained unchanged until Rozeboom & Komp (1950) treated Melanoconion and Mochlostyrax as a single subgenus. Lane (1953) followed Rozeboom & Komp's classification but resurrected Tinolestes from synonymy with Melanoconion as a separated subgenus. A year later, Foote (1954) determined that Mochlostyrax was distinct based on larval morphology and considered it to be a subgenus separate from Melanoconion. Foote's separation of Mochlostyrax and Melanoconion prevailed until Belkin (1968), Belkin et al. (1970) and Sirivanakarn (1983) considered Melanoconion and Mochlostyrax to form a single subgenus.
Dyar (1928) recognised four sections in subgenus Mochlostyrax, the Dinoporpa, Helcoporpa, Mochlostyrax and Choeroporpa sections, and four sections in subgenus Melanoconion, the Tinolestes, Gnophodeomyia, Melanoconion and Anoedioporpa sections. Edwards (1932) recognised subgenus Mochlostyrax, without sections, and divided subgenus Melanoconion into three groups (Groups A, B and C) based on external features of adults. Rozeboom & Komp (1950) disagreed with Edwards's classification and largely adopted Dyar's (1928) scheme based chiefly on features of the male genitalia for their concept of subgenus Melanoconion, which included Mochlostyrax and excluded Anoedioporpa. Hence, Rozeboom & Komp divided the subgenus into seven sections, namely the Choeroporpa, Dinoporpa, Gnophodeomyia, Helcoporpa, Melanoconion, Mochlostyrax and Tinolestes sections. Nearly two decades later, Galindo (1969) established the Spissipes Group based on male genitalia and larval characters and Duret (1969) recognised the Ocellatus Group based on distinctive features of adults and male genitalia. Both groups were retained and redefined in the revised scheme of classification proposed by Sirivanakarn (1983).
Sirivanakarn (1983) distinguished three sections within the subgenus, the Melanoconion, Ocellatus and Spissipes Sections, and divided the Melanoconion and Spissipes Sections into Groups and Subgroups based principally on structural differences of the male genitalia, characteristics of the scaling on the head and scutum of adults and features of the larvae. Pecor et al. (1992) removed the Ocellatus Section from the subgenus, and it remains without subgeneric placement within genus Culex. More recently, Sallum & Forattini (1996) refined the Spissipes Section to include eight Groups and three Subgroups.