When Mr Flowers appeared in court, he wore a grey hoodie with “off the grid” written on it. Mr Jubair sat next to him, wearing a black hoodie and black glasses.
Neither man spoke to each other during the proceedings.
Deputy Director Paul Foster, head of the NCA’s National Cyber Crime Unit, said: “Today’s charges are a key step in what has been a lengthy and complex investigation.
“This attack caused significant disruption and millions in losses to TfL, part of the UK’s critical national infrastructure.”
The hack disrupted TfL services for three months.
TfL wrote to around 5,000 customers to say there may have been unauthorised access to their personal information such as bank account numbers and sort codes.
Data including names, emails and home addresses had been accessed, TfL added.
Earlier this year, the NCA warned of an increasing threat from cyber criminal gangs based in the UK and other English-speaking countries, of which Scattered Spider is an example.