Mutants of an attenuated Bacillus anthracis (ΔANR) strain conferring increasing levels of ciprofloxacin resistance have been described. Here, we report the draft genome sequences of the parent strain (ΔANR pXO1-, pXO2-) and its derivatives conferring low (step 1; 0.5 μg/ml), medium (step 2; 8 to 16 μg/ml), and high (step 3; 32 to 64 μg/ml) levels of ciprofloxacin resistance.