Introduction: The clinical relevance of Achromobacter xylosoxidans infection in cystic fibrosis (CF) remains controversial. This emerging agent in CF has been associated with increased lung inflammation, more frequent exacerbations and more severe lung disease. We describe a pair of CF siblings chronically colonized by the same multilocus genotype of A. xylosoxidans with different clinical courses, and assess whether this species may have developed any virulence traits and antimicrobial resistance that could have contributed to their singular outcomes. Case presentation: Two siblings were positive for the F508del and Y1092X mutations, and were chronically colonized by Pseudomonas aeruginosa and Staphylococcus aureus. The female patient had a more severe CF phenotype and faster clinical deterioration than her brother. Her pulmonary function and computed tomography scan lesions were worse than those of her brother, and both parameters progressively declined. She died at 14 years of age, when he was 18. All isolates of A. xylosoxidans were biofilm producers. Achromobacter xylosoxidans showed less swarming motility in the female patient. Conclusions: Biofilm production and diminution of motility allow persistence. Only swarming motility differed between the isolates recovered from the two siblings, but this finding is not sufficient to explain the different clinical outcomes despite their similar genotypes. Modifier genes, unknown environmental factors and female gender can partially explain differences between these siblings. We were unable to correlate any microbiological findings with their clinical courses, and more translational studies are necessary to decrease the gap of knowledge between laboratory and clinical data to promote better clinical interventions.