Trichodiniasis is one of the major diseases found in fish worldwide. However, little is known regarding the effects of parasitism according to the life stage of the host in captivity. Moreover, there is a lack of knowledge regarding the treatment of parasitic infections of fish. In this study, taxonomic identification (morphological and morphometric description) of trichodinids in Brazil and a comparison of parasitism in larvae and juveniles were performed using scanning electron microscopy, and the effectiveness of treatment with formaldehyde and sodium chloride was assessed. Six species of trichodinids (Trichodina centrostrigata, Trichodina migala, Trichodina heterodentata, Trichodina compacta, Tripartiella orthodens and Paratrichodina africana) were identified as parasites of Nile tilapia. The larvae showed a greater number of alterations, which were also more severe compared with juveniles. The outer surfaces of the infected larvae (integument, eye and fins) were highly affected, whereas the juveniles were rarely affected. A conventional treatment protocol using formaldehyde (1 mL L− 1) and sodium chloride (1%) for 15 min was highly effective. However, a protocol using half the amount of the disinfectant showed similar results (p > 0.05), whereas another protocol (using one quarter the amount of formaldehyde) was less effective than both of these protocols (p < 0.05). The results achieved here provide the first report of T. migala and T. orthodens in South America. The findings regarding the parasite:host relationship suggests that fish larviculture is highly affected and hence should be the main area of focus for the prevention and control of this type of parasitism. Preventive measures and indoor production strategies during the first days of fish hatching are highly recommended. Furthermore, this study shows that half the amount of formaldehyde than conventionally used can achieve the same efficacy in the treatment of trichodiniasis.