Henneguya Thélohan, 1892 (additional source)
Henneguya aegea Katharios, Varvarigos, Keklikoglou, Ruetten, Sojan, Akter, Cascarano, Tsertou & Kokkari, 2020 (additional source)
Henneguya aequidens Videira, Velasco, Azevedo, Silva, Gonçalves, Matos & Matos, 2015 (additional source)
Henneguya bagre Mirandola Dias Vieira, Bravin Narciso & Da Silva, 2022 (additional source)
Henneguya bicaudi Kaur & Attri, 2015 (additional source)
Henneguya brachypomus Capodifoglio, Adriano, Naldoni, Meira, Da Silva & Maia, 2020 (additional source)
Henneguya breviscauda Mirandola Dias Vieira, Bravin Narciso & Da Silva, 2022 (additional source)
Henneguya bulbosus Rosser, Griffin, Quiniou, Khoo & Pote, 2014 (additional source)
Henneguya calcarifer Borkhanuddin, Cech, Molnár, Shaharom-Harrison, Khoa, Samshuri, Mazelan, Atkinson & Székely, 2020 (additional source)
Henneguya carolina Rocha, Casal, Garcia, Matos, Al-Quraishy & Azevedo, 2014 (additional source)
Henneguya cartilaginis Yokoyama, Urawa, Grabner & Shirakashi, 2012 (additional source)
Henneguya collaris Morsy, Semmler, Al-Olayan & Mehlhorn, 2016 (additional source)
Henneguya cuniculator Naldoni, Maia, Silva & Adriano, 2014 (additional source)
Henneguya fastigata Vieira, Narciso, De Azevedo & Da Silva, 2022 (additional source)
Henneguya gilbert Casal, São Clemente, Lopes, Rocha, Felizardo, Oliveira, Al-Quraishy & Azevedo, 2017 (additional source)
Henneguya jaczoi Székely, Borzák & Molnár, 2018 (additional source)
Henneguya jariensis Zatti, Atkinson, Maia, Bartholomew & Adriano, 2018 (additional source)
Henneguya jocu Azevedo, Rocha, Matos, Matos, Oliveira, Al-Quraishy & Casal, 2014 (additional source)
Henneguya jundiai Negrelli, Vieira, Tagliavini, Abdallah & De Azevedo, 2019 (additional source)
Henneguya lacustris Vieira, Rangel, Tagliavini, Abdallah, Santos & De Azevedo, 2020 (additional source)
Henneguya lagunensis De Azevedo, Negrelli, De Oliveira, Abdallah, Camara, Matos & Vieira, 2021 (additional source)
Henneguya lambariensis Margarido, Adriano, Valladão, Naldoni & Pilarski, 2021 (additional source)
Henneguya laseeae Leis, Rosser, Baumgartner & Griffin, 2016 (additional source)
Henneguya lata Chinh, Ngo, Van Tuc, Itoh, Yoshinaga, Shirakashi & Doanh, 2021 (additional source)
Henneguya latiusii Gupta & Kaur, 2018 (additional source)
Henneguya lepturus Azevedo, Feltran, Rocha, Matos, Maciel, Oliveira, Al-Quraishy & Casal, 2018 (additional source)
Henneguya longisporoplasma Zatti, Marinho, Adriano & Maia, 2022 (additional source)
Henneguya loretoensis Mathews, Naldoni & Adriano, 2017 (additional source)
Henneguya maculosus Carriero, Adriano, Silva, Ceccarelli & Maia, 2013 (additional source)
Henneguya marcquenskiae Leis, Rosser, Baumgartner & Griffin, 2019 (additional source)
Henneguya mauritaniensis Khlifa, Miller, Adlard, Faye & Sasal, 2012 (additional source)
Henneguya melini Mathews, Maia & Adriano, 2016 (additional source)
Henneguya michiganensis Rosser, Loch, Faisal, Baumgartner & Griffin, 2021 (additional source)
Henneguya mississippiensis Rosser, Griffin, Quiniou, Khoo, Greenway, Wise & Pote, 2015 (additional source)
Henneguya multiradiatus Mathews, Mertins, Espinoza, Milanin, Alama-Bermejo, Audebert & Morandini, 2020 (additional source)
Henneguya nagelli De Azevedo, Abdallah, Paes, Da Silva, Matos, Velasco & Matos, 2013 (additional source)
Henneguya novaerae Mirandola Dias Vieira, Bravin Narciso & Da Silva, 2022 (additional source)
Henneguya ogawai Li, Sato, Kamata, Ohnishi & Sugita-Konishi, 2012 (additional source)
Henneguya ovata Liu, Xu, Luo, Zhao, Liu, Zhang & Zhang, 2018 (additional source)
Henneguya paranaensis Eiras, Pavanelli & Takemoto, 2004 (additional source)
Henneguya pardensis Vieira, Narciso, De Azevedo & Da Silva, 2022 (additional source)
Henneguya peruviensis Mathews, Mertins, Pereira, Maia & Adriano, 2018 (additional source)
Henneguya pindaibensis Úngari, Vieira, Alcantara, Emmerich, Santos, Silva & O'Dwyer, 2020 (additional source)
Henneguya polarislonga Jorge, Vieira, Zago, Franceschini & Da Silva, 2022 (additional source)
Henneguya quelen Abrunhosa, Sindeaux-Neto, Hamoy & Matos, 2018 (additional source)
Henneguya rotunda Moreira, Adriano, Silva, Ceccarelli & Maia, 2014 (additional source)
Henneguya sacacaensis Ferreira, Silva, Araújo, Hamoy, Matos & Videira, 2020 (additional source)
Henneguya santarenensis Naldoni, Maia, Correa, Silva & Adriano, 2018 (additional source)
Henneguya sarotherodoni Fall, Fomena, Kostoïngué, Diebakate, Faye & Toguebaye, 2000 (additional source)
Henneguya setiuensis Borkhanuddin, Cech, Molnár, Shaharom-Harrison, Khoa, Samshuri, Mazelan, Atkinson & Székely, 2020 (additional source)
Henneguya sinova Özer, Özkan, Gürkanlı, Yurakhno & Çiftçi, 2016 (additional source)
Henneguya tapajoensis Zatti, Atkinson, Maia, Bartholomew & Adriano, 2018 (additional source)
Henneguya tapariensis Capodifoglio, Meira, Da Silva, Corrêa, Adriano & Maia, 2020 (additional source)
Henneguya tietensis Vieira, Rangel, Tagliavini, Abdallah, Santos & De Azevedo, 2020 (additional source)
Henneguya tucunarei Zatti, Atkinson, Maia, Bartholomew & Adriano, 2018 (additional source)
Henneguya unitaeniata Úngari, Vieira, da Silva, Santos, de Azevedo & O'Dwyer, 2019 (additional source)
Henneguya visibilis Moreira, Adriano, Silva, Ceccarelli & Maia, 2013 (additional source)
Henneguya voronini Borkhanuddin, Cech, Molnár, Shaharom-Harrison, Khoa, Samshuri, Mazelan, Atkinson & Székely, 2020 (additional source)
Henneguya yokoyamai Li, Sato, Kamata, Ohnishi & Sugita-Konishi, 2012 (additional source)