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A shrine is where Shinto is practiced. A temple is where Buddhism is practiced. A simple way to distinguish is if there is a guard frame, called Torii(鳥居), in the entrance or not.  A shrine has a Torii, and a temple doesn’t have it. Tori is a gate, which is composed of two wooden pillars supported by two horizontal wooden bars.Shinto and Buddhism date back to thousands of years.Shinto, a spiritual principle, is an ancient religion of Japan based on the belief that powerful deities called kami (神 gods) inhabit both heaven and earth.

Mixture of Shinto and Buddhism (Shinbutsu shugo)
Meanwhile,the mixture of Shinto and Buddhism is called “Shinbutsu shugo (神仏習合),” a kind of intuitional harmonizing of the two faiths that took place from about A.D. 710 to 1868.
It is also called Shinbutsu konkō (神仏混淆, "jumbling up" or "contamination of kami and buddhas"), is the syncretism of Buddhism and kami worship that was Japan's only organized religion up until the Meiji period. Beginning in 1868, the new Meiji government approved a series of laws that separated Japanese native kami worship, on one side, from Buddhism which had assimilated it, on the other.
When Buddhism was introduced from China in the Asuka period (6th century), rather than discarding the old belief system, the Japanese tried to reconcile the two, assuming both were true. As a consequence, Buddhist temples (寺, tera) were attached to local Shinto shrines (神社,jinja) and vice versa and devoted to both kami and buddhas. The local religion and foreign Buddhism never quite fused, but remained however inextricably linked all the way to the present day, always interacting. The depth of the resulting influence of Buddhism on local religious beliefs can be seen for example in the fact that much of Shinto's conceptual vocabulary and even the types of Shinto shrines we see today, with a large worship hall and religious images, are themselves of Buddhist origin.]The formal separation of Buddhism from Shinto took place only as recently as the end of the 19th century; however, in many ways, the blending of the two still continue.

Separation of Buddhism from Shinto (shinbutsu kakuri)
In fact, the term shinbutsu kakuri (神仏隔離 isolation of "kami" from Buddhism) in Japanese Buddhist terminogy refers to the tendency that existed in Japan to keep some kami separate from Buddhism. While some kami were integrated in Buddhism, others (or at times even the same kami in a different context) were kept systematically away from Buddhism. This phenomenon had significant consequences for Japanese culture as a whole.It must not be confused with shinbutsu bunri ("separation of kami and buddhas") or with haibutsu kishaku("abolish buddhas and destroy Shākyamuni"), which are phenomena recurrent in Japanese history and usually due to political causes. While the first assumes the acceptance of Buddhism, the second and third actually oppose it.

Kami and Buddhism Separation Order (神仏判然令 Shinbutsu Hanzenrei)
During the Shinbutsu kakuri, the attempt to separate Shinto from Buddhism, temples and shrines were forcefully separated by law with the "Kami and Buddhism Separation Order" (神仏判然令 Shinbutsu Hanzenrei) of 1868.

However, in spite of more than a century of formal separation of the two religions, temples or shrines that do not separate them are still common, as proven for example by the existence of some important Buddhist Inari shrines. During the Meiji period, in order to help the spread of Shinto, shrine-temples (jingū-ji) were destroyed while temple-shrines (chinjusha) were tolerated. As a result, shrine-temples are now rare (an extant example is Seiganto-ji), but temple-shrines are common, and most temples still have at least a small one.
Prominent religious institutions in both camps still give evidence of integration of the two religions. The great Kenchō-ji temple, number one of the Kamakura's great Zen temples (the Five Mountain System) includes two shrines. One of the islands in the right-side pond of Tsurugaoka Hachimangū in Kamakura hosts a subshrine dedicated to goddess Benzaiten, a form of Saraswati.For this reason, the sub-shrine was removed in 1868 at the time of the Shinbutsu Bunri, but rebuilt in 1956.

Shinto and Buddhism still have a symbiotic relationship of interdependence, particularly concerning funeral rites (entrusted to Buddhism) and weddings (usually left to Shinto or sometimes Christianity). The separation of the two religions is therefore considered only superficial, and shinbutsu shūgō is still an accepted practice.
Still, the separation of the two religions is felt to be real by the public. Scholar Karen Smyers comments, "The surprise of many of my informants regarding the existence of Buddhist Inari temples shows the success of the government's attempt to create separate conceptual categories regarding sites and certain identities, although practice remains multiple and nonexclusive".