Technically, the answer to your question can be "yes". That is it is a machlokes as to what exactly the mitzvah is.
We can also say that the answer can be technically "no", in that it is not necessarily an "either or" situation.
We basically treat it as a single mitzvah with 49 parts. That is, we say the mitzvah each day (even though we cannot be certain that we will complete it), but we do not continue with the bracha if we do miss a day (safek bracha lehakel). However, we do continue saying it (without a bracha) if we miss a day.
There is also a machlokes whether or not it is currently a Torah Mitzvah (since it is explicitly commanded) or a rabbinic mitzvah (since it is connected with korbon omer which we can no longer bring).
This actually brings up the case of the bar mitzvah boy or a ger who become chayav mitzvos in the middle of the omer period. Whether or not it is one long mitzvah or 49 separate mitzvos will make a difference in the halacha. Also whether the mitzva today is rabbinic or not will make a difference. In fact there can be logic that would allow the bar mitzvah boy to continue saying with a bracha, but not allow the ger to start saying with a bracha. There is also logic to allow both to say with a bracha or to prevent both from saying with a bracha.
A Sefirah Dilemma
The Mitzvah of Counting the Omer
1) In the Temple Era, when the Beis Ha-Mikdash stood and the
Omer offering was brought, there was a Torah mitzvah to count the Omer
Count, which spans from the bringing of the offering until the
festival of Shavuos, as the verse states: “You shall count for
yourselves from the morrow of the Sabbath, from the day on which you
brought the Omer offering—seven complete weeks they shall be—until the
morrow of the seventh week, you shall count fifty days.”
2) In times when the Temple does not stand, and the Omer
offering is not brought, rishonim dispute concerning whether the Torah
mitzvah of counting the Omer applies, or whether the obligation is
3) Most authorities maintain that in the absence of the
Temple, the mitzvah is only a rabbinic enactment. Nevertheless, one
must follow stringencies based on the opinions that counting is a
4) Rishonim also dispute whether or not a distinct mitzvah of
counting the Omer applies each day, or whether the entire counting
period is included in one continuous mitzvah.
A Separate Mitzvah Count Each Day or One 49 Day Counting Mitzvah?
There is quite an interesting discussion amongst the Gaonim and
Rishonim regarding the nature of the counting of the Omer in terms of
seeing each day as a separate mitzvah or seeing the entire 7 weeks as
one big mitzvah. There are three main approaches in the Rishonim to
Tosafos , The Rosh , and Rav Hai Gaon  explain that there is no
clear indication in the verses to support the conclusion that this is
one 49 Day Mitzvah. Rather each day of counting is a mitzvah in its
own right. The concept of temimos indicates that the counting should
be done at night and perhaps has other ramifications but isn’t
relevant to this particular point.
Rav Yehudai Gaon  explains that due to the tenet of temimos the
entire counting of all 49 days must also be complete. That is to say
that if a person misses counting one day out of the 49 he has thus
lost the entire mitzvah of counting the Omer.
Rav Sadyah Gaon  takes a position somewhat in the middle. He agrees
with Rav Yehudai Gaon to a degree that all 49 days are bound together
as one and require temimos. However, the limit of this qualification
is only with regards to starting the count on the 16th of Nissan. If a
person counts the first night of the Omer correctly, then even if he
misses other nights during the rest of the 49 days we look at it as if
he is “still in the process of counting 49 days from the 16th of
Nissan. However, if a person missed counting the first night on the
16th of Nissan then he has lost the entire opportunity to fulfill this
mitzvah for this year. The reason is because once he missed the first
night we can no longer see him as being “in the process” of counting
the 49 days from the 16th of Nissan until Shavuos.
The Shulchan Aruch  writes that the halacha lemaseh is that if a
person missed a day of counting (both night and subsequent day) he
must still keep counting for the rest of the 49 days but he may not
make a blessing out of deference to the opinions that this is One 49
The Terumas Hadeshen  writes that if a person has a doubt as to
whether he counted on a particular day (i.e. he is truly uncertain one
way or another whether he counted) in such a case since there is a
double doubt he may continue to count on the remaining days with a
blessing. The rationale is that maybe the halacha follows the Tosafos
and the Rosh, and even if it follows the Gaonim it is possible that he
counted yesterday. This is in fact the halacha Lemaseh found in
Another outgrowth of this disagreement relates to a person who
converted to Judaism or even a young boy he became 13 during the
middle of the Omer period. According to the view that it is a separate
mitzvah each day then he may surely count from the point at which he
becomes obligated in mitzvos. If it is one long 49 day mitzvah then
how can he achieve temimos in which case he should count the rest of
the time without a bracha.
The prevailing custom regarding a Bar Mitzvah is that provided he
started the count when he was still before Bar Mitzvah he can continue
the rest of the count with a bracha. The rationale here is that
perhaps the halacha is like those who say each day is a separate
mitzvah and furthermore, there are poskim who add another facet that
since until now the boy wasn’t obligated, so from here on if he counts
without missing that is called temimos for him.
. ↑ Gemara Menachos 66a “Zecher” and Megillah 20b “Kol Halaylah”
. ↑ Pesachim Ch 10 Siman 41
. ↑ See Maharitz Geus Vol 2 pg 109 and Tshuvos Hagaonim Vol 2 pg 212
. ↑ Ba’al Halachos Gedolos “Atzeres”
. ↑ Sidddur Harasag pg 155
. ↑ Orach Chaim 489:8
. ↑ Vol 1 Siman 37
The obligation to count the Omer
Biblically, it only applies in Temple times (when the Omer offering
is brought) but we continue to perform it today by rabbinic enactment.
This mitzvah is discussed in the Talmud in tractate Menachos on page
66a and is codified in the Shulchan Aruch in Orach Chaim 489. It is #161
of the 248 positive mitzvos in the Rambam’s Sefer HaMitzvos and #26 of the
77 positive mitzvos that can be fulfilled today as listed in the Chofetz
Chaim’s Sefer HaMitzvos HaKatzar.
Sefiras Haomer Connects thie mitzvah of Sefiras Haomer to the mitzvah of tefillin. Rabbi Winston explains that the mitzvah of tefillin is renewed each day that that there is no question about saying the bracha even if a day has been missed.
At the root of this discussion is one’s understanding of the mitzvah
of Sefiras HaOmer: is it one long, continuous mitzvah with fifty
parts, or, does each day’s counting stand as a separate mitzvah? If
the former, then the blessing has been lost because the mitzvah is no
longer complete (though you still count each subsequent day without
its blessing); if the latter, then, what was, was, but, what is coming
up is what counts now and therefore, say the blessing.
When it comes to Tefillin, a mitzvah that is also performed most days,
missing one day does not change tomorrow’s obligation in any way. What
was missed is lost, but, every new day is a new chance to do the same
mitzvah, and therefore all blessings must be said. How many single
mitzvos are there that are performed over such a long period of time?
Halachically, we have decided to treat Sefiras HaOmer, which lasts
over FORTY-NINE days, like a single mitzvah, which means miss a day,
lose the blessing for the rest of the counting. It’s a phenomenal
concept which certainly puts pressure on males to make sure that, for
forty-nine days, they do not forget to count the omer — which some do,
for one reason or another!
However, one can understand why when comparing the mitzvah of
Tefillin, for example, and, the mitzvah to count the omer. Tefillin is
the same mitzvah each and every day, though, one should be using that
‘same mitzvah’ to grow spiritually so that, the next time Tefillin are
worn, it is a different, spiritually more elevated act than all other
times before. However, the actual performance of the mitzvah remains
Not so with Sefiras HaOmer, for, though each day the counting-process
is the same, the wording is different for each count, revealing an
obvious build-up toward the holiday of Shavuos. The Omer-Count is a
spiritual construction process, whereby the end result justifies all
the ‘work’ and ‘expenditure’ until that end-result is realized.