Natalie McGarry, the MP for Glasgow East, has been charged with fraud offences following an investigation by Police Scotland.
It is understood the alleged offences are linked to her involvement with the group Women for Independence, which was set up in the run-up to the 2014 Scottish referendum, and with the SNP's Glasgow Regional Association.
The amount of money allegedly involved is a five-figure sum, according to sources.
A Police Scotland spokeswoman said: "On Tuesday September 27, a 35-year-old woman was charged in connection with alleged fraud offences.
"A report will be sent to the procurator fiscal."
McGarry was elected as the SNP MP for the Glasgow East constituency in May 2015, when Nicola Sturgeon's party won all but three of the 59 Scottish seats at Westminster.
In November she withdrew from the party whip as police continued to investigate concerns over missing donations from the prominent pro-independence group she helped set up.
As a result she was automatically suspended from the party, and she currently sits as an independent MP in the House of Commons.
Women for Independence said on Twitter: "We will be making no public comment on today's news."
McGarry has previously insisted there has been "no wrongdoing on her part".