The perennial sciaphilous alga Phyllophora crispa (Phyllophoraceae, Rhodophyta) belongs to the main community-forming species of the Black Sea but due to the catastrophic degradation of its populations, it has been listed as an endangered species in the Red Data Book of the Russian Federation. Phyllophora crispa off the southwestern coast of Crimea is preserved within six Protected Areas (PAs) established between 1972 and 2017, which include the narrow 300-m-wide strips of coastal waters ranging from 0.0597 km2 to 0.208 km2 in area. Despite a long existence, the degeneration of P. crispa assemblages has been shown in some of them that may indicate inefficient measures aimed at conserving bottom communities in Marine PAs (MPAs) and the need to optimise the regional PA network. Therefore, this study addresses assessing the effectiveness of the preservation of P. crispa in MPAs along the southwestern coast of Crimea, and it aims at two main objectives: to compare the status of P. crispa populations in the study area at present and before the MPA establishment, and to assess their current state in the marine protected and unprotected areas. In 2015–2020, the density, biomass, weight and length of P. crispa thalli were determined in five MPAs ranged in age 33–48 years of protection and in 16 unprotected water areas, at depths from 0.5 m to 20 m. A comparison of the obtained and published data for the 5 m to 20 m depth range showed that from 1964–1967 until 2015–2020, the P. crispa biomass in the study area decreased on average 2.7-fold, the density 1.5-fold and the thallus weight 2.0-fold. Evaluating the decline of the populations of P. crispa along the depth range of 5–15 m showed that it was most pronounced at a 15-m depth, being statistically significant in biomass and thallus weight. At the same time, an analysis of variance showed no effect of protection on the between-year change in P. crispa population parameters. In addition, in 2015–2020, there was no statistically significant difference in the average biomass and density of this species inside and outside the MPAs. The average weight and length of thalli did not differ due to protection either, except for a depth of 10 m where values of these parameters were, respectively, 3.3 times and 1.4 times higher inside than outside MPAs. One explanation for the non-significant MPA effect on the state of populations of P. crispa could be a lack of statistical power in our study. Another one was the small area and low width of MPAs, which makes the seaweed communities vulnerable to negative impacts near the MPA borders. To improve the effectiveness of the conservation of P. crispa in the southwestern Crimea, it was recommended to increase the MPA coverage, create buffer zones around MPAs and take measures resulting in environmental improvement throughout the region.