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This study investigated the prevalence and the potential risk factors for anxiety and depression among physiotherapists during the pandemic. Physiotherapists answered a web-based questionnaire including 1) sociodemographic, professional and clinical information; 2) psychosocial demands; and 3) two validated questionnaires to measure anxiety and depression. Binary logistic regression identified the risk factors by means of odds ratio (OR) and 95% confidence interval (CI). In 417 participants, there was a high prevalence of anxiety (48.2%) and depression (53.0%). The risk factors for anxiety were female sex (OR 2.07; 95%CI 1.01-4.24), worsening in sleep patterns (OR 3.78; 95%CI 1.92-7.44), moderate (OR 2.24; 95%CI 1.00-5.00) and extreme concern about financial issues (OR 3.47; 95%CI 1.57-7.65), and extreme loneliness (OR 3.47; 95%CI 1.71-7.07). The risk factors for depression were female sex (OR 2.16; 95%CI 1.03-4.55), low family income (OR 2.43; 95%CI 1.21-4.89), worsening in sleep patterns (OR 5.97; 95%CI 3.02-11.82), extreme concern about financial issues (OR 2.61; 95%CI 1.15-5.94), and extreme loneliness (OR 4.38; 95%CI 2.00-9.63). This study found a high prevalence of anxiety and depression in the studied population and identified risk factors for both.