Two new species of particular biogeographic significance are described from the upper rio Paraguay basin, one of the genus Paracanthopoma (Trichomycteridae, Vandelliinae) and the other of the genus Ernstichthys (Aspredinidae, Hoplomyzontinae). The two species occur sympatrically in the Rio Taquarizinho, tributary of the Rio Taquari, in the upper Paraguay system. Paracanthopoma saci is distinguished from its only congener, P. parva, by a spatulate caudal peduncle; a minuscule premaxillary dentition (reduced to three delicate teeth); the supraorbital latero-sensory canals opening as two separate s6 pores; the caudal fin slightly convex or truncate with round edges; the skull roof entirely open, unossified; the origins of dorsal and anal fins approximately at same vertical; and the pelvic fin with three rays. Ernstichthys taquari is diagnosed among congeners by the narrow bony shields on dorsal and ventral series, not overlapping or contacting each other; by the presence of seven or eight serrations on the posterior margin of the pectoral spine; and by the pectoral-fin spine only slightly larger than subsequent soft rays. Both Paracanthopoma and Ernstichthys were previously unknown outside of the Greater Amazonian river systems (Amazon, Orinoco, Essequibo and smaller surrounding drainages). Their presence restricted to the Rio Taquari is unexpected and suggests a peculiar biogeographical history. Ancestral geographic distributions were reconstructed using S-DIVA and BBM methods in RASP. A majority of resulting hypotheses support that the two species reached the Paraguay from the Amazon. The alternative explanation accounts for their presence in the Paraguay by vicariant events. In no case, their presence in the Paraguay is an ancestral distribution with subsequent Amazonian dispersal. Though unusual, this pattern is also seen in a few other fish taxa, showing that the Rio Taquari is biogeographically hybrid, combining elements from both the Paraguay and Amazon drainages.