Conservation: Amphilophus istlanus is evaluated by the international union for the conservation of nature in the iucn red list of threatened species as (LC) least concern (2018). A. istlanus faces multiple threats from urban and industrial pollution, habitat degradation, water extraction, hydropower, dam construction, potential overfishing, aquarium trade extraction, and foreign species invasion. However, this species is widespread and occurs within many protected areas of Mexico, and it is not thought that there is a global population decline (Daniels, 2019).

In the Amacuzac River, Balsas drainage, I witnessed A. istlanus sharp population decline in the late 1980s after the introduction of the convict cichlid, Amatitlania nigrofasciata, which quickly colonized the river. Trujillo-Jiménez (1998) found that A. nigrofasciata has a wider but partially overlapping diet with the more specialized A. istlanus, but she rules out that diet alone has displaced the native species.