Purpose With the rapid development of e-commerce, logistics demand is increasing day by day. The modern warehousing with a multi-agent system as the core comes into being. This paper aims to study the task allocation and path-planning (TAPP) problem as required by the multi-agent warehouse system. Design/methodology/approach The TAPP problem targets to minimize the makespan by allocating tasks to the agents and planning collision-free paths for the agents. This paper presents the Hierarchical Genetic Highways Algorithm (HGHA), a hierarchical algorithm combining optimization and multi-agent path-finding (MAPF). The top-level is the genetic algorithm (GA), allocating tasks to agents in an optimized way. The lower level is the so-called highways local repair (HLR) process, avoiding the collisions by local repairment if and only if conflicts arise. Findings Experiments demonstrate that HGHA performs faster and more efficient for the warehouse scenario than max multi-flow. This paper also applies HGHA to TAPP instances with a hundred agents and a thousand storage locations in a customized warehouse simulation platform with MultiBots. Originality/value This paper formulates the multi-agent warehousing distribution problem, TAPP. The HGHA based on hierarchical architecture solves the TAPP accurately and quickly. Verifying the HGHA by the large-scale multi-agent simulation platform MultiBots.