ABSTRACT: Climate change has the potential to alter the abundance and distribution of coastal foundational species worldwide through range expansions. However, there is comparatively little evidence to show how climate change may alter interactions between foundational species that already co-occur. Here, we use long-term environmental monitoring data and non-parametric models to identify the factors driving the local cover of 2 co-existing foundational seagrasses, Zostera marina and Ruppia maritima, across 38 non-consecutive years in Chesapeake Bay, USA. We show, from an analysis of cover along permanent transects in the lower, polyhaline areas of the bay, an altered relationship between the abundance of these 2 species through time and space: mean cover on these transects of Z. marina was 47% in the 1990s, declined to 19% in the 2000s, and further declined to 17% in the 2010s, indicating a general decline of about 64% over the past 3 decades. In contrast, R. maritima cover was generally lower and less variable than Z. marina cover and increased from 6.8% in the 1990s to 7.5% in the 2000s and finally to 11.4% in the 2010s. Generalized additive models revealed that, after accounting for other environmental covariates, the cover of one species was strongly influenced by the cover of the other. The dominance of Z. marina over R. maritima was further modulated by rising temperatures. Thus, we propose that climate change may mediate the distributional patterns of these 2 species to the detriment of Z. marina and the benefit of R. maritima.