Some 32 people were arrested in Puglia, Sicily, Campania, Calabria, Lazio, Abruzzo, Marche, Emilia Romagna, Veneto and, abroad, in Germany, France, Netherlands and Malta.
Those probed are suspected of conspiracy, trafficking, making slaves of women, extortion, robbery, bodily harm, sexual violence and exploitation of prostitution, police said.
The probe was led by Bari anti-mafia prosecutors and coordinated by the central operational service in Rome with the help of Interpol.
The investigation was carried out by the Bari flying squad.
Much of the trafficking and drug dealing allegedly took place in the vast CARA asylum seeker centre in Bari.
The two clans were the Supreme Vikings Confraternity and the Supreme Eye Confraternity, better known as "Reds" e "Blues".
The gangs operated with the slogan "the three Ds", referring to "donne, denaro e droga" (women, money and drugs).
Some 49 people were placed under investigation, all Nigerian nationals. The bust was hailed by politicians including Brothers of Italy (FdI) leader Giorgia Meloni who said "we must extirpate this cancer" and League MP Rossano Sasso who said the probe had highlighted the need, yet again, to close down the CARA asylum seeker centre in Bari.
Bari prosecutor Francesco Giannella commented the operation on Tuesday saying the case should not be ''exploited'' politically. ''The Nigerians who were arrested are people who committed a crime'' exactly like ''people of any color, race and country''.
There are ''many Nigerians who asked for help according to the law, in other words they asked the Italian State to intervene to bring back order and justice'', he said.
Bari's chief prosecutor Giuseppe Volpe also stressed that many Nigerian nationals cooperated in the investigation. ''Many of the crimes' victims are also Nigerian citizens who cooperated'' with investigators, noted the chief prosecutor.
''I want to highlight this because often we have a hard time obtaining the cooperation of the local population'', he said.
The investigation kicked off at the end of 2016 after two victims said they were beaten up by clan members because they refused to become members of one of the gangs.
Evidence in the case includes two letters asking authorities for help, dating back to March and May 2017. The letters were sent to police by the spiritual pastor of Bari's asylum seeker reception center (CARA) and by some of the migrants staying there who felt threatened by the presence of gang members who controlled the facility.
''Please protect us because, by providing information, we are endangering our lives'', wrote the pastor. ''We implore the Italian government to protect us because we were not safe in Nigeria, we fled for this reason, and now we are not safe in this center'' due to the clans.
Investigators said the women, most of them trafficked and subjected to physical and psychological violence, also via voodoo rites, were forced to become sex workers.
The proceeds of the prostitution rackets were sent to Nigeria via couriers or 'hawala' systems, or reinvested in drug trafficking.
The probe found an exponential rise in cash flows from Italy to Nigeria, which was estimated by the Bank of Italy at 74.79 million euros in 2018, double what it had been in 2016, and consisting of 6.2 million illegal proceeds per month.
Investigators compared this to the numbers of Nigerians in Italy, equal to 105,000 as of June 30 this year - most of them men, with a lower employment rate (45.1%) than the general non-EU population (59.1%) and the highest unemployment rate (34.2% compared to 14.9% of non EU nationals).