Studying fish communities in extreme habitats is important to better understand the variation in their ranges under climatic scenarios or anthropogenic pressure. In particular, the mangroves in Baja California Sur occupy the northernmost distribution range under two extreme conditions (temperate waters and arid weather). In this context, the aim of the presently reported study was to analyze the functional characteristics of ichthyofauna in two localities, La Paz Bay (BP) and Almejas Bay (BA), which are also located in different ecoregions. For both bays, the composition and frequency values were compiled from monthly samples and the literature. Eleven functional traits were assessed from the morphology of every fish species. Functional indices (Richness, Evenness, Divergence, and Originality) were used to evaluate different aspects of the community structure. A total of 83 species were found at both sites, with 54 in BP and 50 in BA. In BP, six species were residents, eight were temporal visitors, and 36 were occasional visitors. In BA, six species were residents, 15 species were temporal visitors, and 33 were occasional visitors. At both sites, 12% of the species were permanent residents; BA had a higher percentage of temporal residents (27%), while BP had a higher percentage of occasional visitors (72%). The functional analysis detected communities with specialized traits, but in comparison to BP, BA had higher evenness in the community structure. Although greater structural complexity was expected in the community during the warm months, because of the increase in richness and attributes, BA had higher values during the cold months, which was probably because the area is a transition zone and the fish communities are adapted to colder climates. In comparison to BA, BP had higher originality values, and colder months presented higher values than warmer months. Although the mangrove sites had the same northernmost latitudinal limits and both had extreme conditions compared to those in mangroves in tropical environments, the fish communities differed in their composition, frequency, and functionality with more extreme functional traits in colder weather than in warmer weather.