Eigenmannia waiwai differs from other members of the E. trilineata species group by having the length of anterodorsal process of maxilla equal to 1.5 times the width of the posterior nostril (vs. equal to 50% of the width of posterior nostril in E. antonioi, E. desantanai, E. guairaca, E. muirapinima, E. pavulagem, and E. vicentespelaea, or equal to the width of the posterior nostril in E. matintapereira, E. microstoma, and E. trilineata). In addition, it is distinguished from other species of the E. trilineata species group, with the exception of E. vicentespelaea, by having subterminal mouth (vs. terminal mouth). It can be diagnosed from E. vicentespelaea by having nine or ten longitudinal series of scales above the lateral line (vs. seven or eight), body depth at the vertical through the tip of longest pectoral-fin ray, 14.9-18.7% LEA (vs. 10.5-14.5%), depth of the posterodorsal expansion on infraorbitals 1 + 2 less than 50% of length of infraorbitals 1 + 2 (vs. approximately equal to length of infraorbitals 1 + 2), and length of the coronomeckelian bone equal to 20% of the length of Meckel’s cartilage (vs. 45% of the length of Meckel’s cartilage) (Ref. 115689).