Morphological, behavioural, immunological, and general line performance traits have been used in genetic monitoring of standard lines. Molecular marker sets are now used to map genetic traits in zebrafish and have been used in other species for genetic monitoring. These sets should be useful in determining the degree of inbreeding within a line (to optimise maintenance), determining the loss of genetic variation per generation (to reduce inbreeding), and identifying contamination by other fish lines. This method of monitoring for contamination assumes that line-specific alleles are not present elsewhere in the facility. Similar strategies can be used to measure residual background when introgressing alleles into a new background and to accelerate the process by selecting statistical outliers with the lowest residual background. Contamination of a breeding stock with other fish is commonly regarded as the most damaging disruption to a genetic line. Fortunately, it is one of the most avoidable. The most common causes are human error and escaped animals, both of which should be avoidable through design and training measures. Screening families every generation and keeping reproductively isolated and redundant copies of the line in parallel are two methods for removing unwanted alleles. Before breeding, each population will be genetically monitored to determine whether it should be eliminated or propagated. If one is removed, the propagated group should be split to restore redundancy. For large breeding populations, such redundancies can be handled more efficiently by housing families separately and testing them before breeding. This strategy, combined with close monitoring, should eliminate the majority of unwanted genetic events. Inbreeding will increase slightly if 10% of the families are removed and the line is propagated with the remaining 90% of the families. To compensate for the reduced size of the Vective population, the total number of families maintained could be increased.