Although a parapoxvirus harmful to red squirrels is present in UK squirrel populations it is not considered a major cause of red squirrel decline, and replacement by the introduced grey squirrel, since diseased individuals are rarely observed. Such assumptions, equating a low visibility of disease to a correspondingly low importance at the population scale, are common in conservation biology. Here we demonstrate that this is a fallacy. Our model indicates that parapoxvirus has played a crucial role in the red squirrel decline.