Atlantirivulus paranaguensis can be diagnosed from all its congeners by the

following combination of characters: lateral line divided into two sections (vs. single); lateral line with one neuromast by scale (vs. lateral line often interrupted by scales without neuromasts); caudal fin oval in both sexes (vs. sub-truncate at least in males); caudal fin margins in males with high concentration of melanophores, forming a well-delimited black ventral margin about thrice wider than a black dorsal margin (vs. melanophores, when highly concentrated, forming diffuse black zones on the entire caudal fin, darker and slightly wider on the ventral portion); venter white (vs. yellow); caudal-fin spot always conspicuous in females (vs. spot pale or absent in females above 2.8 cm SL) (Ref. 102354).