Species name should be italicised. I had exactly the same issue using a reference manager in a recently submitted paper, and I had to correct all species names manually. It is worth to be alert about the citation as a whole. For example, some journals require that other journals names are abbreviated in the reference list. I have noticed that such abbreviations are sometimes wrongly made.

I'm not sure if my first response was added, so I'll write again. The names of the species should be italicised. I had exactly the same problem with a paper I recently submitted, and I had to correct it manually. It is worth staying alert with the rest of references as a whole. For example, some journals require that the other journals name are abbreviated. I have also noticed that sometimes the reference manager inserts the abbreviation wrongly.

Yes, genus and species names should be in Italic in an article title. However, if it's in a book title and the journal format is such that the rest of the title is Italic, then the scientific name alone must not be Italic. There are other ways to address this, but probably easiest done manually.

Dear Alham,

In old botanical literature Scholars used to write Latin in sloping form. Since then it has become a custom to write botanical Latin in italics [see Lawrence, George H. M., Taxonomy of Vascular Plants. New York: The Macmillan Company, 1951]. Many a things depend up on the Editorial style, I think it is better to write the scientific names [which are in Latin] in italics if it not against the editorial guidelines.

With best wishes,

Subir.

Dear Walid

Yes it is mandatory to write the scientific names of the biological species in italics,  for this you may follow the rules of the ICN and the link as mentioned by Dr. Subir Bandyopadhyay.

With regards

Sunit.

Thank you so much all, The answers are very helpful.

Alham:

Please have a look at this link for helpful guidance:

http://blog.vancouvereditor.com/2011/03/science-writing-and-editing-scientific.html

Best

Syed

Dear Mr. Sayed,

That you so much, that was very helpful.

Best Regards

Elham

Just to add, the italics are used for binomial nomenclature anywhere because the italics conveys the information that you're actually talking about a biological species. Otherwise, you've lost that important bit of information.

You should italicize all species names even in the references. It helps much when you go through a long reference list and most periodicals request tis way of typing.

Different journals have different formats. Some italicize titles of books, some do not. Some italicize names of journals, some do not. Scientific names should be as in the publication being cited. If the name is italicized in the title of the paper being cited, the name should be italicized in the your References or Literature Cited section. If the name is not italicized in the title, do not italicize the name in the References or Literature Cited.

Check the journal reference requirements, usually they have some samples, if not, check some of the published articles by the journal and see how the scientific names were listed.  Work with the rules of the ICZN and the Journal samples.

This depends on the journal. Each journal has its own requirements. The best thing would be to see some recent articles, or (best) check the journal's Instructions to Authors.

Thank you all for those valuable answers 

Check the various scientific journals as they have different formats. Follow the rules and regulations of ICZN and Journals format including the instructions to authors.

You should italicize the binomial names in your research paper even in the Reference sections.