Comey said that during the calls, Mateen also mentioned Moner Mohammad Abusalha, a fellow Floridian who had travelled to Syria to fight with Jabhat al-Nusra, the al-Qaeda affiliate in Syria. Mateen had been investigated by the FBI for his contact with Abusalha in 2014, but the case was quickly closed. Abusalha returned to Syria, where he killed himself in a suicide attack.
Further confusing matters, Comey also revealed that in "inflammatory and contradictory" comments to co-workers in 2013, Mateen had claimed to be a member of Hizbollah, the Shia militia based in Lebanon.
To be clear, these groups named by Mateen are NOT allies.
Isis and al-Qaeda both derive their theology from an extreme view of Sunni Islamism, but in practical terms the pair split in 2014, with the more established al-Qaeda publicly disavowing the actions of the more extreme Isis.
Jabhat al-Nusra, al-Qaeda's affiliate in Syria, often fights Isis in the Syrian conflict.
Hizbollah is a Shia Islamist group. In Syria, it supports the Government of Bashar al-Assad, effectively meaning it fights both Isis and al-Qaeda.
Comey suggested that Mateen may have not understood the distinctions among the groups.
Relatives have given mixed reports about the level of Mateen's religiosity, with some suggesting he preferred working out to studying religion.
He attended the Islamic Centre of Fort Pierce, Florida, though he is said to have rarely spoken. His Afghan father has filmed videos that appeared to offer support for the Taliban, a fundamentalist movement that also opposes Isis, though his messages also were sometimes incoherent.
Mateen certainly wouldn't be the first terrorist to cite Islam as justification for his actions while apparently being somewhat confused about the religion.
In one especially notorious case, two British men who were found guilty of terrorism charges in 2014 ordered Islam for Dummies, The Koran for Dummies and Arabic for Dummies from Amazon before they left for Syria.