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Abstract Background Rheumatoid arthritis is the most common type of inflammatory arthritis affecting about 1% of the population. With the advent of disease-modifying anti-rheumatic drugs the disease can be well controlled in many cases. Patients, however, are prone to developing infectious complications. In rare cases, these can mimic a flare of the underlying itself. Case presentation We report the case of a 45-year-old female patient with a history of seronegative rheumatoid arthritis (RA) who presented with swelling and tenderness of the third metacarpophalangeal joint of the right hand. A flare of her RA was suspected based on clinical and ultrasound findings which showed a tenosynovitis with intense power doppler activity. Her steroid dose was increased but the clinical response to glucocorticoid therapy was very limited. Subsequently, she developed skin manifestations of ‘swimmer’s granuloma’ over the next 2 weeks after first presentation. Finally, a diagnosis of a Mycobacterium marinum infection was established with the help of tissue biopsy and culture, and the patient received appropriate antibiotic treatment with the desired effect. Conclusions This case highlights the difficulty of distinction between infection and inflammation in patients with joint swelling and pain, especially in the age of disease-modifying drugs (DMARDs) and the concomitant risk of atypical infections. A review of the literature identified eight additional published cases, which suggests that Mycobacterium marinum infection is a rare but recognized complication of DMARD therapy. It can mimic a flare of the underlying arthritis potentially leading to diagnostic delays, and requires differential diagnostic methods to identify the pathogen and pave the way for appropriate treatment.