Current DRAM-based memory systems face the scalability challenges in terms of memory density, energy consumption, and monetary cost. Hybrid memory architectures composed of emerging Non-Volatile Memory (NVM) and DRAM is a promising approach to large-capacity and energy-efficient main memory. However, hybrid memory systems pose a new challenge to on-chip cache management due to the asymmetrical penalty of memory access to DRAM and NVM in case of cache misses. Cache hit rate is no longer an effective metric for evaluating memory access performance in hybrid memory systems. Current cache replacement policies that aim to improve cache hit rate are not efficient either. In this paper, we take into account the asymmetry of cache miss penalty on DRAM and NVM, and advocate a more general metric, Average Memory Access Time (AMAT), to evaluate the performance of hybrid memories. We propose a miss penalty aware LRU-based (MALRU) cache replacement policy for hybrid memory systems. MALRU is aware of the source (DRAM or NVM) of missing blocks and preserves high-latency NVM blocks as well as low-latency DRAM blocks with good temporal locality in the last level cache. Experimental results show that MALRU can improve system performance by up to 22.8% and 13.1%, compared to LRU and the state-of-theart HAP policy, respectively.