Different species of algae may grow in different places. Where algae grow depends mainly on the types and concentration of accessory pigments possessed by different kinds of algae. Different accessory pigments need different quality and intensity of light. The change of light wavelength thus affects the distribution of the algae. Generally speaking, in darker areas or the deep ocean, phycoerythrin and phycocyanobilin can absorb blue light more effectively than chlorophyll a. Thus green algae, which contain mainly chlorophyll a and β-carotene, usually inhabit in shallow water regions. The zonation of algae is most obvious near the coastal areas. Green algae are usually found in the upper littoral zone. Brown algae are mostly found in the middle littoral zone, whereas red algae are commonly seen in the lower littoral zone or in the deep ocean.
Substrate, topography, temperature, salinity, humidity, tides, waves, wind, currents and pollutants can all affect the growth and distribution of the algae, just as light can. Some algae prefer the areas with strong waves; others prefer calm water or sea bays. Some can tolerate drier conditions, so they can grow in the supralittoral fringe; others can survive in the extraordinal environmental changes (dry or wet) in the littoral zone, in which occurs low tide twice daily. The algae growth varies depending on the substrate, such as lithoherm, coral reefs, stone blocks, shells and mud. Certain types of algae even accrete with other marine organisms. In general, algae tend to grow on lithoherm or coral reefs in the coastal regions, especially in tidal pools or reef grooves. Hence, these areas are the best places to collect algae. In Taiwan, it is easier to collect and to observe algae in northern and northeast Taiwan, Hengchun Peninsula and the islands like Lanyu, Green Island, Penghu Archipelago and Siao-Liou-ciou. The coastlines along western Taiwan are mostly sandy beaches. As their substrates can be easily eroded by waves, sand beaches are not suitable for algal growth. The east coastlines of Taiwan are mostly scarps, which cause lot of difficulties to collect algae.
Most algae present in Taiwan are annual. The marine macroalgal flora in the littoral zone has obvious seasonal changes. Algae usually flourish in winter and spring. In summer and autumn, the algae decrease significantly in richness and species. Particularly in summer, when strong sunlight and high temperature make it difficult for algae to survive, algae are often absent in the littoral zone. One can only find some algae in deeper waters.
The Kuroshio Current with warm water and high salinity goes through the coastlines of southern Taiwan while the northern coast of Taiwan is influenced by the cold China Coastal Current. As a result, marine macroalgae flora in southern is quite different to that in northern Taiwan. For example, the north is known the home for temperate marine algae, such as Porphyra crispata, Bangia atropurpurea and Gelidium amansii, which are absent in the south. On the other hand, in the south, in places like Hengchun Peninsula, Siao-Liou-ciou, Lanyu and Green Island, one can find tropical algae, such as Codium arabicum, Halimeda opuntia, Caulerpa brachypus f. parvifolia and Boergesenia forbesii.