Moore was suspended by League One Rovers on February 17 after an investigation was launched by the FA's Football Integrity Unit.
The club posted a statement on their website on Monday afternoon confirming that the 61-year-old had now been charged.
It read: "The FA has charged Ronnie Moore for alleged multiple breaches of Rule E8(b) for misconduct in relation to betting.
"The Tranmere Rovers manager has until 8 April 2014 to respond to the charges.
"The club will make no further comment at this time."
Assistant manager John McMahon has been in temporary charge at Prenton Park during Moore's suspension, with Tranmere currently 20th in the table, one place above the relegation zone on goals scored.
Current regulations prohibit players, managers and club officials from betting on competitions in which their teams are involved.