Macroautophagy (hereafter autophagy) is a catabolic process by which autophagosomes arising from an isolation membrane fuse with lysosomes to degrade components in the cytoplasm. Autophagosome-lysosome fusion step is one of the key steps during the process of macroautophagy. The step is extremely complicated and its detailed mechanisms remain unclear. It consists of two phases: first phase is autophagosome migration phase and second phase is fusion of autophagosomes and lysosomes phase. Recently, various molecules have been reported to be involved in each phase. In the first phase, microtubules and actin remodeling mechanism are involved. In the second phase, soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins, Rab family proteins, phosphoinositide 3-kinase (PI3K) complex and Rubicon are involved. In the present review, we introduce recent findings related to autophagosome-lysosome fusion step and discuss liver diseases possibly associated with autophagosome-lysosome fusion dysfunction.