This paper documents the occurrence of the exotic South American suckermouth armoured catfishes (Loricariidae) of the genus Pterygoplichthys spp. in the drainages of Thiruvananthapuram City, Kerala. The morphological taxonomy revealed that the specimens are closely related to Pterygoplichthys disjunctivus (Weber, 1991) and P. pardalis (Castelnau, 1855), in addition to intermediary forms of unknown identity. DNA barcoding using the mitochondrial DNA cytochrome c oxidase 1 (CO1) also failed to establish the identity of the invaded species. There may be possible hybridisation in aquariums or in fish farms or in the wild, but this needs to be found out aided by detailed studies incorporating different molecular markers and with sequences of topotypes. The possible threats due to Pterygoplichthys spp. invasion and management options are discussed in the paper.