Kalpana; Oops! My finger slipped... (Pinus radiata) grows along the coast in California. Those individuals that grow near the sea cliffs are bent over, small and look like Banzai trees. Those that grow in protected places a short way inland are taller and have a more typical pine shape...morphotypes. I think that the term implies only a distinctive form.
Ecotypes...The different forms of the plant in different habitat types are both morphologically distinguishable but also are genetically distinct. Also from California a small shrub, Eriogonum fasciculatum, grows in both coastal and desert habitats. The coastal populations are larger and also have a different ploidy number than to the desert populations.
a population is group of individuals of a species which live in a given area.
Your samples being taken from different places, they are samples from different populations.
A morphotype is a subunit of a species, which is individualized by one or a few morphological characters (as compared to the morphologye of the species nomenclaaural type). A morphotype is usually due to one or a few mutations.
An ecotype is a morphotype encountered in a particular ecology.
Hi Kalpana, I must say that I agree with Marc's response.
Given that your questions do not provide background about if there are really morphological or genetic differences between your study sites, "populations" looks like the most proper term.