Abstract: The present application discloses a method and apparatus for processing a file in a distributed system. A specific implementation of the method includes: receiving a file having predetermined identifiers; splitting the file into a plurality of subfiles based on a size of the file, a number of the predetermined identifiers in the file and a number of servers in the distributed system, each of the plurality of subfiles comprising an identical number of the predetermined identifiers; and sending, in response to a file processing request sent by at least one of the servers in the distributed system, the plurality of subfiles to a corresponding server for parallel processing of the file. This implementation improves the processing efficiency of a genetic information file, and implements load balancing.