Saccocoelioides is a genus of trematodes associated with fishes from the Americas. In the current research, morphologically distinct specimens of Saccocoelioides spp. were collected from six countries in Middle America. Specimens were sequenced using three molecular markers, the domains D1–D3 of the large subunit (LSU) from the nuclear rDNA, the cytochrome c oxidase subunit 1 (cox1) and nicotinamide adenine dinucleotide dehydrogenase subunit 1 (nad1) from mitochondrial DNA. A total of 74 new sequences were compared and aligned with other sequences available in GenBank. Maximum likelihood and Bayesian inference analyses were inferred from the LSU and cox1 datasets, revealing unequivocally that all the specimens correspond to S. lamothei. A haplotype network was built with 119 sequences of the nad1 gene. The network detected 57 distinct haplotypes divided into three haplogroups. To explore morphological differences among samples of S. lamothei, 17 morphological features were measured from 53 specimens from three fish families: Eleotridae, Mugilidae and Gobiidae. Principal component analysis yielded three main polygons that corresponded with each family analysed, suggesting host-induced phenotypic plasticity. The current evidence suggests that S. lamothei infects at least five fish families along the Pacific coasts of Mexico, Guatemala, El Salvador, Honduras, Nicaragua and Costa Rica.