ABSTRACT Lagrangian particle tracking models are considered an important tool for assessing connectivity in the deep sea. A number of user interfaces are available to assess oceanic structural connectivity. These use currents produced by state-of-the-art ocean models, and can be used to run forward/hindcast simulations, habitat connectivity calculations, comparison of physical circulation models, etc. We compared simulation outputs from two particle tracking packages, WebDrogue v.0.7 and the Parcels framework version 2.1, the former having been previously published in a study investigating connectivity patterns among closed areas in the NAFO Regulatory Area. We further tested a combination of parameters used by Parcels (number of particles, particle spacing, time step, random walk) to determine optimal values for future applications. Parcels identified more connectivity than WebDrogue with differences attributed to higher current velocities in the underlying ocean model, although drift pathways were ... : ACKNOWLEDGMENTS. This project was supported by Fisheries and Oceans, Canada's International Governance Strategy (IGS) Research Fund, with funding to EK. Also, this research has been performed as a contribution to the SponGES project, which received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No. 679849. Dr. Shuangqiang Wang's contribution was funded through the Postdoctoral Research Program led by Natural Resources Canada, in collaboration with Fisheries and Oceans Canada. We thank Drs. Trevor Kenchington and F. Javier Murillo Perez (Fisheries & Oceans, Canada, Bedford Insitute of Oceanography) for their careful review of this Report. © Her Majesty the Queen in Right of Canada, 2019. Correct citation for this publication: Wang, S., Wang, Z., Lirette, C., Davies, A. and Kenchington, E. 2019. Comparison of Physical Connectivity Particle Tracking Models in the Flemish Cap Region. Can. Tech. Rep. Fish. Aquat. Sci. 3353: v + 39 p. Canadian Technical ...