© 2015 The Authors. We present a new method of finding protoclusters using tomographic maps of Ly α forest flux. We review our method of creating tomographic flux maps and discuss our new highperformance implementation, which makes large reconstructions computationally feasible. Using a large N-body simulation, we illustrate how protoclusters create large-scale flux decrements, roughly 10 h-1 Mpc across, and how we can use this signal to find them in flux maps. We test the performance of our protocluster finding method by running it on the ideal, noiseless map and tomographic reconstructions from mock surveys, and comparing to the halo catalogue. Using the noiseless map, we find protocluster candidates with about 90 per cent purity, and recover about 75 per cent of the protoclusters that form massive clusters (>3 × 1014 h-1M⊙). We construct mock surveys similar to the ongoing COSMOS Lyman-Alpha Mapping And Tomography Observations survey. While the existing data have an average sightline separation of 2.3 h-1 Mpc, we test separations of 2-6 h-1 Mpc to see what can be tolerated for our application. Using reconstructed maps from small separation mock surveys, the protocluster candidate purity and completeness are very close to what was found in the noiseless case. As the sightline separation increases, the purity and completeness decrease, although they remain much higher than we initially expected. We extended our test cases to mock surveys with an average separation of 15 h-1 Mpc, meant to reproduce high source density areas of the Baryon Oscillation Spectroscopic Survey. We find that even with such a large sightline separation, the method can still be used to find some of the largest protoclusters.