The objective of this study consists to conduct the first monitoring of seagrass meadows and two non-indigenous species (NIS) in the associated benthos (<em>Bursatella leachii</em> and <em>Callinectes sapidus</em>) as indicators of the Integrated Monitoring and Assessment Program (IMAP) in the Ramsar site of the Marchica lagoon located on the north-eastern coast of Morocco. This lagoon has been the focus of a succession of restoration actions since 2010 aimed at conserving its biodiversity and improving its environmental state. Thirty sampling stations were monitored during the 2022-2023 winter season to determine the spatial distribution of seagrass meadows and of two non-Indigenous species above mentioned. Our results showed the presence of two marine species <em>Cymodocea nodosa</em>, the most widespread species, and <em>Zostera noltei</em>. The spatial distribution revealed the presence of the species only on the borders of the lagoon and their absence in the central area. For NIS, the results showed 143 <em>Callinectes sapidus</em> and 45 <em>Bursatella leachii </em>in different sizes ranging from small to large. To protect the marine phanerogams in the Marchica lagoon, it is recommended to develop this preliminary study by a spatiotemporal survey considering a seasonal pattern (winter, spring, summer and autumn) and by monitoring others stations in order to examine the existence of other species of seagrass and identified the benthos associated. The results of field monitoring will be used for future seagrass monitoring using satellite remote sensing as recommended by IMAP guidelines.