The frequencies of a cryogenic sapphire oscillator and a hydrogen maser are compared to set new constraints on a possible violation of Lorentz invariance. We give a detailed description of microwave resonators operating in Whispering Gallery modes and then apply it to derive explicit models for Lorentz violating effects in our experiment. Models are calculated in the theoretical framework of Robertson, Mansouri and Sexl and in the standard model extension (SME) of Kostelecky and co-workers. We constrain the parameters of the Mansouri and Sexl test theory to and which is of the same order as the best results from other experiments for the former and represents a 70 fold improvement for the latter. These results correspond to an improvement of our previously published limits [Wolf P. et al., Phys. Rev. Lett. {\bf 90}, 6, 060402, (2003)] by about a factor 2.

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