The Humboldt Current System (HCS) is characterised by latitudinal upwelling differences and interannual El Niño events that bring equatorial warm waters into the system. Within the HCS, the silverside Odontesthes regia is a coastal fish that faces intense harvesting, and physical and oceanographic variability. Here, we evaluated how different processes in the HCS have shaped the spatial and temporal genetic variation of O. regia populations by using 650-bp alignment of the mitochondrial control region and nine microsatellite loci. We found that both DNA markers indicated high genetic diversity, presence of at least two co-distributed genetic groups, and a slight genetic structure shaped by a biogeographic break within the HCS rather than the latitudinal upwelling differences or geographical distances. Demographic history of these groups suggests an allopatric origin and posterior reconnection as the result of historical changes in the HCS. No genetic interannual divergences were found in subsystems with intermittent presence of warm waters, suggesting no significant influence of El Niño on the genetic variation of O. regia from 2013 to 2018. Despite the inherent disturbances of the HCS, past and recent estimates of effective population sizes showed high values in most populations. Our results provide essential information for the management of O. regia in the HCS. Our study also helps to understand how the spatio-temporal dynamics of the HCS influences the genetic variation of coastal marine fishes.

洪堡海流系统 (HCS) 的特点是纬度上涌差异和年际厄尔尼诺事件将赤道温水带入系统。在 HCS 中，silverside Odontesthes regia是一种沿海鱼类，面临着大量捕捞以及物理和海洋变化。在这里，我们评估了 HCS 中的不同过程如何影响O. regia 的时空遗传变异通过使用线粒体控制区和 9 个微卫星位点的 650 bp 比对来确定种群。我们发现这两个 DNA 标记都表明了高遗传多样性，至少存在两个共同分布的遗传组，以及由 HCS 内的生物地理断裂而不是纬度上升流差异或地理距离形成的轻微遗传结构。这些群体的人口统计学历史表明，HCS 历史变化的结果是异域起源和后部重新连接。在间歇性存在温水的子系统中未发现遗传年际差异，表明厄尔尼诺现象对O. regia的遗传变异没有显着影响从 2013 年到 2018 年。尽管 HCS 存在固有干扰，但过去和最近对有效种群规模的估计在大多数种群中显示出较高的值。我们的结果为HCS中O. regia的管理提供了重要信息。我们的研究还有助于了解 HCS 的时空动态如何影响沿海海洋鱼类的遗传变异。