The objectives of this study were to compare four risk assessment protocols for non-native species in neotropical regions and to assess the potential application of these tools for the management of invasive species and conservation of the ichthyofauna in Brazil. The protocols Fish Invasiveness Screening Kit (FISK), Aquatic Species Invasiveness Screening Kit (AS-ISK), European Non-Native Species in Aquaculture Risk Assessment Scheme (ENSARS) and Fish Invasiveness Screening Test (FIST) were applied for the species Oreochromis niloticus, Coptodon rendalli, Poecilia reticulata and Apteronotus aff. albifrons, whose sources of introduction are aquaculture and fishkeeping. The species were classified as low, medium or high risk of invasion. The scores of the species O. niloticus, C. rendalli and P. reticulata classified them as high risk of invasion in all protocols, whereas A. aff. albifrons had medium risk in the protocols FISK and AS-ISK and low risk in the FIST. Although the results were similar for species whose impacts are widely described, less studied species may have their classification compromised by the lack of evidences in the literature. Despite the difficulties for practical application, the use of these tools may be encouraged, considering the potential threats of other invasive species emerging in Brazil. The comparison between the methods showed that the use of AS-ISK, combined with ENSARS in cases of introductions by aquaculture, provides important answers about ecological impacts on natural environments and about the stages of the aquaculture production chain that should be better inspected.