To determine the prevalence of fibromyalgia (FM) in patients with ankylosing spondylitis (AS) or psoriatic arthritis (PsA) characterized by axial involvement (axial-PsA), and to assess the discriminative ability of different versions of the Ankylosing Spondylitis Disease Activity Score (ASDAS) and the Bath Ankylosing Spondylitis Activity Disease Activity Index (BASDAI) in measuring disease activity in three different cohorts of patients with axial spondyloarthritis (axial-SpA), FM, or both (axial-SpA + FM), this study was divided into two phases: (1) 402 patients with definite AS or axial-PsA were examined to diagnose FM and estimate its prevalence; and (2) 419 patients (111 with axial-SpA, 248 with FM, and 60 with aSpA + FM) were evaluated using the different versions of the ASDAS and BASDAI to assess the effect on disease activity. The overall prevalence of FM in the axial-SpA population was 14.9 %, significantly higher among women (p < 0.0001); the estimated prevalence in AS was 12.7 % and in axial-PsA was 17.2 %. Although the BASDAI scores correlated with those of ASDAS-C-reactive protein (CRP) and ASDAS-erythrocyte sedimentation rate (ESR) (p < 0.0001), only ASDAS had sufficient discriminatory ability to assess disease activity. The addition of only one marker of inflammation led to an adequate level of significance (ASDAS-CRP, p = 0.0018; ASDAS-ESR, p = 0.003). FM is common in axial-SpA and more prevalent in female patients. Our findings suggest that ASDAS is better than BASDAI in distinguishing patients with disease activity from those with functional impairment. The use of ASDAS may be very useful in clinical practice as it allows treating patients with the most appropriate therapy.