The Texaco Station at the corner of Range Street and Ross Clark Circle was held up around 11:30 p.m. Tuesday.
Police say the clerk had just closed for the night when she was confronted in the parking lot by a masked man with a gun.
The suspect stole the woman's car, her purse and a bank bag containing the store's money.
The vehicle was found abandoned at a Dothan housing complex about a half hour later.
No one was injured in the incident.
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