Catalyst coated membrane [CCM] type and catalyst coated substrate [CCS] type of membrane electrode assembly [MEA] were manufactured and evaluated their performance. Degradation test were conducted to find the difference of long term stability in two types of MEA and the factor for performance degradation problem occurred. Performance degradation test of single cell in two different types of MEA were carried out when current density was $200mA/cm^{2}$. The degradation test had proceeded for 230 hours and performance degradation was checked by I-V curve and impedance measurement at regular intervals. Also, MEA before/after operation and changes of catalyst layer were characterized by SEM, TEM, and XRD. Maximum power density of CCM type was higher than that of CCS type. Meanwhile, an increase of particle size of catalyst and an increase of impedance resistance after long term operation were observed. In the case of using CCM type MEA, the performance was deteriorated 38% of initial performance. In the case of using CCS type MEA, the performance was deteriorated 43% of initial performance. In consideration of difference of initial performance, performance of CCM type is higher than that of CCS type but both types had similar problems during degradation test.