Information about ploidy is important in both commercial and conservation aquaculture and fish research. Unfortunately, methods for its determination, such as karyology, determination of the amount of DNA in a cell using microdensitometry or flow cytometry and/or measuring erythrocytes in a blood smear can be stressful or even destructive. Some of these methods are also limited by the relatively large minimum size of the individual being measured. The aim of this study was to test a new low-stress method of determining ploidy by measuring the size of erythrocytes in the capillaries of a fish, including small individuals. First, we examined diploid and triploid loach (Cobitis sp.) and gibel carp, Carassius gibelio (Bloch, 1782), using flow cytometry and blood smears, with these results being used as a control. Subsequently, we measured the size of erythrocytes in the caudal fin capillaries of anesthetized fishes of known ploidy under a light microscope. For both the loaches and gibel carp, direct observation of the mean erythrocyte size in epithelial fin capillaries provided a consistent and reliable determination of ploidy when compared with the controls based on flow cytometry and blood smears. This new method allows for rapid determination of ploidy in living small fish, where collection of tissue using other methods may cause excessive stress or damage. The method outlined here simply requires the measurement of erythrocytes directly in the bloodstream of a live fish, thereby making it possible to determine ploidy without the need for blood sampling. The method described is sufficiently efficient, less demanding on equipment than many other procedures, can be used by relatively inexperienced personnel and has benefits as regards animal welfare, which is especially important for fish production facilities or when dealing with rare or endangered species.