Significance All genes are duplicated by whole-genome duplication (WGD), reverting in number over time, but the actual timing of genome reshaping through gene loss remains poorly understood. We estimated the spatiotemporal loss/persistence pattern of 6,892 gene lineage pairs after the teleost-specific WGD, using careful orthology assignment and a reliable time-calibrated tree. We found that massive gene loss did occur in the first 60 My, mainly due to events involving the simultaneous loss of multiple redundant genes, and the rate of loss then slowed to an approximately constant level for the subsequent 250 My. Similar genomic gene arrangements within teleosts imply that rapid gene loss led to the reshaping of the teleost genomes before their major divergence.