We present a database of microfossil fragmentation and nannofossil assemblages during the Paleocene-Eocene transition at ODP Site 1209 leg 198 (North Pacific). We propose a new method based on nannofossil fragment counts to reconstruct an all-inclusive nannofossil absolute abundances (entire nannofossils plus fragments). Using nannofossil assemblages and foraminiferal-based dissolution proxies we detect a 400 kyrs dissolution event occurring some 300 kyrs before the Paleocene-Eocene Thermal Maximum.A total of 56 samples were analysed using a scanning electron microscope (SEM) and 28 were analysed with a light-polarized microscope. Samples were prepared using a slightly modified version of the settling method described by Beaufort et al. (2014; doi:10.1038/nprot.2014.028). For each sample, the depth (slightly modified from Westerhold et al. (2018; doi:10.1029/2017PA003306), weight and studied surface area are reported. The counts, absolute and relative abundances of entire nannofossils and fragment groups benefit from a confidence interval at 95% (calculated according to Suchéras-Marx et al., 2019; doi:10.1016/j.marmicro.2019.101751) as well as the nannofossil fragmentation. A statistical treatment (Analysis of Variance) of the main nannofossil groups was performed using the software Past4.0 to compare the results of the analysis performed using SEM and light-polarized microscope. The reconstruction of nannofossil abundance using the different categories of placolith fragments is provided with the 95% confidence interval.Overgrown and dissolution were assessed using a Discoaster spp. overgrowth scale based on Dedert et al. (2014; doi:0.1016/j.marmicro.2013.12.004) and dissolution proxies (planktonic foraminifera fragmentation %, benthic/planktonic ratio %, sediment coarse fraction %). All these proxies have a 95% confidence interval except the coarse fraction from which the weighting error is provided. Finally, our database includes 73 bulk carbonate isotope measurements of the δ13C and δ18O.