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   Abstract In cosmologies with hidden sector dark matter, the lightest hidden sector species can come to dominate the energy budget of the universe and cause an early matter-dominated era (EMDE). EMDEs amplify the matter power spectrum on small scales, leading to dense, early-forming microhalos which massively boost the dark matter annihilation signal. We use the Fermi-LAT measurement of the isotropic gamma-ray background to place limits on the parameter space of hidden sector models with EMDEs. We calculate the amplified annihilation signal by sampling the properties of prompt cusps, which reside at the centers of these microhalos and dominate the signal on account of their steepρ∝r^-3/2density profiles. We also include the portions of the parameter space affected by the gravitational heating that arises from the formation and subsequent destruction of nonlinear structure during the EMDE. We are able to rule out significant portions of the parameter space, particularly at high reheat temperatures. Long EMDEs remain poorly constrained despite large structure-induced boosts to the annihilation signal. 

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