Large branchiopods are specialist crustaceans adapted for life in temporary, thermally dynamic wetland ecosystems. Certain large branchiopod species are, however, restricted to specific temporary wetland types, exemplified by their physico-chemical and hydroperiod characteristics. Here, we contrasted the thermal preference and critical thermal maxima (CTmax) and minima (CTmin) of southern African anostracans and spinicaudatans found exclusively in either temporary rock-pool or pan wetland types. We hypothesized that environment of origin would be a good predictor of thermal preference and critical thermal limits. To test this, Branchiopodopsis tridens (Anostraca) and Leptestheria brevirostris (Spinicaudata) were collected from rock-pool habitats, while Streptocephalus cafer (Anostraca) and a Gondwanalimnadia sp. (Spinicaudata) were collected from pan habitats. In contrast to our hypothesis, taxonomic relatedness was a better predictor of CTmax and temperature preference than environment of origin. Spinicaudatans were significantly more tolerant of high temperatures than anostracans, with L. brevirostris and Gondwanalimnadia sp. median CTmax values of 45.1 °C and 44.1 °C, respectively, followed by S. cafer (42.8 °C) and B. tridens (41.4 °C). Neither environment or taxonomic relatedness were good predictors of CTmin trends, with B. tridens (0.9 °C) and Gondwanalimnadia sp. (2.1 °C) having the lowest median CTmin values, followed by L. brevirostris (3.4 °C) and S. cafer (3.6 °C). On the contrary, temperature preferences differed according to taxa, with spinicaudatans significantly preferring higher temperatures than anostracans. Leptestheria brevirostris and Gondwanalimnadia sp. both spent most time at temperatures 30–32 °C, S. cafer at 18–20 °C and B. tridens at 21–23 °C. Constrained thermal traits reported here suggest that the studied anostracans might be more susceptible to projected climatic warming than the spinicaudatans, irrespective of habitat type, however, these taxa may also compensate through phenotypic plasticity.