A fundamental question regarding the Omer count is whether the mitzvah is Biblical or Rabbinic ever since the Holy Temple was destroyed. The verse says, You shall count for yourselves from the morrow of the “Sabbath” – from the day you bring the Omer of waving – seven weeks; they shall be complete. (VaYikra 23:15).
According to the Rosh, Ran, and many other Rishonim, the Biblical command to count the Omer is in effect only when we offer the Omer of waving on the sixteenth of Nissan, in the Temple. Today, however, when we do not bring this offering, the mitzvah is only Rabbinically ordained. The Rabbis enacted it in commemoration of the Omer count that took place when the Temple stood. This is why we are accustomed to praying for the rebuilding of the Temple after we finish counting. After all, when the Temple is rebuilt, we will [once again] perform the mitzvah on a Biblical level, and not just as a Rabbinic decree.
The Rambam and the Ra’avyah believe that the Omer offering is mentioned [in the verse] only to teach us the date on which the Omer count begins. It is not a necessary condition [for the fulfillment of the mitzvah]. Therefore, we are commanded from the Torah to count the Omer even today when the Temple is in ruins and we are unable to bring the Omer offering.
The practical implication of this halachah concerns situations of doubt. For example, if one counts during the twilight period – that is, between sunset and the emergence of [three medium-sized] stars – it is questionable whether he fulfills the mitzvah of counting. If we consider twilight day, he does not fulfill his obligation, because the time for tomorrow’s count did not yet arrive. If we consider it night, however, he fulfills his obligation. The Aruch HaShulchan (489:2) and the majority of poskim hold that one who counts during twilight fulfills his obligation, because, in their opinion, the Omer count is a Rabbinic mitzvah nowadays, and we rule leniently when a doubt arises [regarding Rabbinic laws]. However, many Acharonim write that it is proper to act strictly and recount, without a blessing, after the emergence of the stars, in order to fulfill the mitzvah even according to those who hold that the Omer count is a Biblical mitzvah nowadays, which requires one to act strictly in cases of doubt (Eliyah Rabbah; M.B. 489:15; B.H. 489:1, s.v. lispor ha’omer).
