The comparability of data from multiple sources is a key factor in ensuring the success of international monitoring programmes such as the EU Water Framework Directive, EC, 2000. This study investigated the effects of using different Lugol’s iodine solutions on marine phytoplankton cell counts, over timescales ranging from 1 day to 8 months of preservation. Samples from cultures of Ditylum brightwellii, Prorocentrum lima, Karenia mikimotoi, Coccolithus pelagicus, Tetraselmis suecica and one (mixed) wild sample were preserved in each of three Lugol’s solutions (neutral, more dilute acidified and less dilute acidified). Cells were enumerated using the Utermohl method, and comparisons were made across preservatives over time. Our results show that no single Lugol’s solution was most effective at limiting cell degradation across all taxa and the relative ratios of taxa may change in a phytoplankton sample as a result of preservation time and preservative used. These findings must be considered when comparing data derived from differently preserved samples. We strongly recommend that published data on marine algal cell concentrations derived from Lugol’s preserved samples must include information on which preservative was used and the lag time between preservation and analysis.