Sili (Macrognathus sp.) is one of freshwater fishes that has high economic value in Asia, since it is beneficial as a consumable fish and an ornamental fish. The economic potential of Sili triggers overfishing, especially in East Java. Domestication is a method to preserve Sili in East Java, preceded by identifying potential species of Macrognathus sp. from the natural catchment. This study aims to characterize the morphological differences of Macrognathus sp in several regencies in East Java based on morphological and morphometric phenotypes. Samples were collected at five different locations, specifically: Tulungagung (Boyolangu Watersheds), Kediri (Brantas Watersheds), Mojokerto (Brantas Watersheds), Lamongan (Bengawan Solo Watersheds), and Malang (Karangkates Reservoir). The main parameters observed were morphology and morphometry. The morphological analysis used identification guidelines, while morphometric data were obtained through 14 parameters measurement then analyzed using one-way Anova test on SPSS 25 software. Based on the morphological and morphometric analysis, it is known that the species of Sili in some regencies in East Java are Macrognathus tapirus and Macrognathus aculeatus. The results showed that samples from Tuban and Kediri are Macrognathus tapirus. Furthermore, the samples collected from Mojokerto, Lamongan, and Malang are Macrognathus aculeatus. One-way Anova test showed Sili from the five locations were significantly different based on the result value of p<0.05.