Flavobacterium columnare (Fc) is the causative agent for columnaris disease (CD) and considered an emerging problem in the Rainbow trout industry. Herein, we characterize the virulence phenotype of two Fc isolates against rainbow trout at the eyed egg and sac fry life stages. Both Fc isolates, CSF-298-10 and MS-FC-4, were isolated from gill tissue of diseased fish and are virulent to juvenile fish >1g in size. The virulence phenotype between these two isolates differed when used for immersion challenges against eyed eggs and sac fry. When sac fry were immersion challenged the CSF-298-10 isolate did resulted in 10 to 38% mortality, depending on the dose used, starting on day 6 post hatch. A total loss of viable sac fry was not recorded till challenged on day 8 post hatch with the CSF-298-10 isolate. The MS-FC-4 produced 80% or greater mortality by day 3 post hatch, and could produce 100% mortality when exposure occurred on day 4 post hatch. When sac fry were immersion challenged with the Fc isolate CSF-298-10 on day 3 post hatch no increase mortality was recorded above mock challenged controls. Similarly, when eyed eggs were exposed to the CSF-298-10 Fc isolate, 3 days pre-hatch, by immersion no increase in mortality was observed over controls. Conversely, immersion exposure of eyed eggs with the MS-FC-4 isolate produced 90% or greater mortality by day 6 post exposure. Mortalities did not start occurring till day 1 post hatch and resulted in greater than 95% mortality regardless of the dose tested. These two Fc isolates present stark differences in virulence phenotypes to both eyed eggs and sac fry and present an interesting model system for virulence kinetics and potentially alternative pathways. Importantly, these results demonstrate the potential problem Fc can have on early life stage rainbow trout production, associated with issues concerning vertical transmission and biosecurity.