Abstract: We compiled the distribution and traits of 214 fish species and subspecies in the Jinsha River basin to investigate systematic and effective conservation planning in the basin. First, we modelled the distribution of widespread species throughout the basin with environmental factors such as climate, riverscape, land-use, and soil type; we used the occurrences as the distribution for other species. We planned the protected area (PA) network with the Marxan software to determine the species-specific conservation targets (grouped by mobility, distribution range, and conservation status) and evaluate the protection status of the current wetlands PAs. The best solution selected 486 planning units (47950 km²) that was 7.7% of the total planning units. The current wetlands PAs was not enough for fish conservation, which shelters 59.3% of all fishes (127 species) and 109 species require additional conservation area. The planning units’ area protected by the wetlands PA need to expand 55.9% to reach our conservation target.