The eelgrass Zostera marina L. is distributed along the Baja California Peninsula and Gulf of California (Mexico) where it is exposed to a wide range of irradiances and temperatures that promote changes in its physiological and biochemical composition. Populations of Z. marina from three coastal lagoons along the Pacific coast, one from the north (San Quintín; SQ) and two from the south (Ojo de Liebre; OL and San Ignacio; SI) of the peninsula were analyzed. Temperature in the southern lagoons was 5–6 ^oC higher than in the northern lagoon. In situ irradiance was two-fold lower at SQ than at OL and SI. As a consequence of the greater irradiance, plants at OL and SI were established 1m deeper with in the water column than those at SQ. While irradiance levels were two-fold greater at the southern lagoons, in general, photosynthetic characteristics were similar among all three lagoons. The hours of light saturated photosynthesis (Hsat), suggest that photosynthesis of shoots from OL and SI are saturated for more than 6 h day^-1 all year, while shoots from SQ are likely light limited during approximately 15% of the year. Consequently, an increase in attenuation coefficient values in the water column will likely decrease light availability to Z. marina plants at SQ, potentially decreasing their survival. Additionally, as a result of the lower irradiance levels, the concentration of chlorophyll and of soluble carbohydrates in the shoots of Z. marina was greater in the northern lagoon than in the southern ones, suggesting that the high levels of chlorophyll are enough to compensate for the low irradiance levels and to maintain a positive carbon balance at SQ. In contrast, the levels of proteins in the shoots at SQ were slightly lower than OL and SI. In general, these results suggest that the different environmental conditions to which Z. marina is exposed along the peninsula impact its biochemical composition. On the other hand, I investigated the genetic characteristics of perennial and annual populations of the marine angiosperm using nine microsatellite loci. Five perennials populations of Z. marina from the Pacific coast of Baja California (PC) and four annual populations from the Gulf of California (GC) were analyzed. The Baja California peninsula represents a biogeographical boundary contributing to regional differentiation (PC vs GC) among populations of marine animals, but nothing is known about marine plants. Analyses of variance revealed significant interregional differentiation, but no subregional (north vs south) differentiation for Z. marina populations. Significant spatial differentiation, assessed using θST values, was observed among all populations within the two regions. Z. marina populations along the PC are separated by more than 220 km and had the greatest (θST=0.13–0.28) values, suggesting restricted gene flow. In contrast, lower but still significant genetic differentiation was observed among GC populations (θST=0.04–0.18), even though populations are separated by more than 250 km. This suggests higher levels of gene flow among GC populations relative to PC populations. Direction of gene flow was predominantly southward among PC populations, whereas no dominant polarity in the GC populations was observed. The test for isolation by distance (IBD) showed a significant correlation between genetic and geographical distances in GC populations, but not in PC populations, perhaps because of shifts incurrents during El Niño Southern Oscillation (ENSO) events along the Pacific coast. Finally, I evaluated the genetic structure of Z. marina in a coastal lagoon (SQ) with restricted water flow, different water residence times and oceanographic characteristics. Analyses of genetic differentiation, (ST), population phylogeny and Bayesian clustering suggest that the Z. marina population in SQ is genetically substructured, with at least four genetically different groups. Genetic structuring can be related to the presence of ecological and physical barriers among the different sites where Z. marina is distributed. While the population was genetically substructured, and a 14% decline of its cover has been detected, this study does not show evidence of a recent bottleneck.