AQUATIC CONSERVATION: MARINE AND FRESHWATER ECOSYSTEMS Aquatic Conserv: Mar. Freshw. Ecosyst. 17: 335–347 (2007) Published online 14 July 2006 in Wiley InterScience (www.interscience.wiley.com) DOI: 10.1002/aqc.776 Alien and endemic flora at reference and non-reference sites in Mediterranean-type streams in Portugal FRANCISCA C. AGUIAR*, M. TERESA FERREIRA, ANTO ´ NIO ALBUQUERQUE and ILI ´ DIO MOREIRA Instituto Superior de Agronomia (Institute of Agronomy), Departamento de Engenharia Florestal, Tapada da Ajuda, Lisbon, Portugal ABSTRACT 1. A comparison was made between a variety of alien and endemic plant species from 272 aquatic and riparian habitats in Portuguese Mediterranean-type streams in reference condition } i.e. near- natural river corridors } and non-reference condition. The objective was to detect differences in relative proportion and cover between these species groups. The differences in endemic and alien flora from siliceous and calcareous river types were also analysed. Environmental and human disturbance factors were related with the richness and cover of both species groups. 2. A total of 568 species were found, of which 44 were alien and 28 were endemic. Alien species were present at 91% of the surveyed locations, and were consistently more widespread at non- reference sites than at reference ones for both river types, with calcareous sites having a higher invasibility. Endemic species occurred at 45% of the sampling sites and displayed a significantly lower richness and cover than their alien counterparts. 3. Alien richness and cover were positively related to direct human disturbance within the river systems, and with floodplain uses such as urban occupation, intensive agriculture, and nutrient inputs. Endemic species also respond to anthropogenic variables, rather than to climatic and geographical ones, with richness and cover increasing as human impacts on fluvial systems and related floodplains decrease. 4. Comprehensive control of alien invasive species and the protection of endemic plant populations will require attempts at monitoring ecological river integrity, and the achievement of ‘good ecological status’ } one of the goals of the European Union’s Water Framework Directive. Portuguese riparian areas must be managed in such a way as to protect the relatively few preserved riparian habitats by lowering the direct and indirect pressures in fluvial corridors and thus preventing future alien plant invasions. Copyright # 2006 John Wiley & Sons, Ltd. Received 8 August 2005; Accepted 11 February 2006 KEY WORDS: invasive species; riparian corridor; species richness; human disturbance; WFD; Iberia; Mediterranean Basin *Correspondence to: Francisca C. Aguiar, Instituto Superior de Agronomia, Departamento de Engenharia Florestal, Tapada da Ajuda, 1349-017 Lisbon, Portugal. E-mail: fraguiar@isa.utl.pt Copyright # 2006 John Wiley & Sons, Ltd.