Both Malaysia and Indonesia have high biodiversity for a variety of organisms, including freshwater red algae. The type localities of over a dozen freshwater red algal taxa are located in Malaysia and Indonesia. These species were described prior to the advent of molecular systematics, and no molecular data were available for specimens from these two countries. Therefore, the goal of this study was to visit type and other locales in Malaysia and Indonesia to recollect freshwater red algal taxa for both morphological and molecular studies. A total of 11 previously published species were identified, with eight taxa belonging to the Batrachospermales, and one each in the Compsopogonales (Compsopogon caeruleus), Ceramiales (Caloglossa beccarii) and Thoreales (Nemalionopsis shawii). The rbcL gene provided numerous insights including two new species, Batrachospermum phangii sp. nov. from Malaysia and Kumanoa celebes sp. nov. from Indonesia. The placement of Batrachospermum cylindrocellulare in section Aristata rather than section Batrachospermum was clarified. Specimens from Malaysia identified as Sirodotia delicatula were distantly related to specimens from South America, suggesting a cryptic species in South America. Likewise, Balliopsis prieurii from Malaysia was distantly related to Balliopsis prieurii from South America. A gametophyte specimen and numerous chantransia stage specimens were conspecific with Batrachospermum macrosporum from South America, and this is a new record of this taxon in Malaysia. Chantransia stage sporophyte specimens from Indonesia had a similar sequence to Sheathia arcuata from Hawaii. The sequence placement of N. shawii from Indonesia points to the need for further systematic research on this genus. Although Kumanoa gibberosa was not recollected at the type location in Malaysia, it was found in Indonesia; likewise, the type locality in Indonesia did not yield S. delicatula but this species was present in Malaysia. Given the previously described diversity, the two new taxa proposed in this study and the insights gained from the present molecular data, we suggest that future focus on freshwater red algae from Southeast Asia will yield considerable knowledge of the flora of the region and freshwater red algal diversity in general.