Population genetic structure in a riverine cichlid fish was recharacterized 2 years after patterns had been first described. We found that genetic structure changed, as evidenced by changes in F(ST) between years among sites, significant F(ST) between years "within" sites, and a significant proportion of the genetic variation partitioned between years. Most striking, signatures of isolation by distance were eradicated between years. Our study highlights that point-in-time estimates of population genetic structure might not be valid over longer time periods, particularly in systems exposed to strong seasonal or interannual variation in abiotic conditions.