While both the Ontario and federal registering of a business give almost identical types of information, the difference is related to geographical jurisdiction and the level of government to which you are registering your business. Business registration in Ontario applies only at the province of Ontario level. You would need to register the business name with the Ontario Government if you operated a business under a name other than your own personal name. In addition, any business having employees, facilities, or offices anywhere in Ontario has to register using the Ontario Business Registry. Depending on the type of business and sector of activity, you may need to get specific licenses and/or permits from the province. You might also need to register for Ontario-specific taxes, including the Ontario Harmonized Sales Tax (HST).
Federal business registration will enable you to work anywhere in Canada. If you want to become incorporated and operate all across the country, then you have to apply by Corporations Canada.
You will also have to have a business number which will be obtained from the CRA for federal tax purposes including GST/HST, along with the payroll deductions and import/export accounts. Federal incorporation gives a corporation the right to operate as such in all provinces and territories under the same name, therefore giving more protection to the name and better brand recognition. You might also need federal licenses or permits based on the nature of your business apart from provincial licenses or permits.
Geographic scope, name protection, and requirements for tax registration create some differences. Ontario registration means the business has its operations limited only to Ontario, while federal registration allows this in all of Canada. Federal incorporates provide protection for a name throughout Canada; Ontario registration protects it within that province. Federal registration requires obtaining a Business Number for federal tax purposes; in the case of Ontario registration, other registrations are required for provincial taxes.
The choice between Ontario and federal registration depends on your business goals, the geographic area you are serving, and how much protection of your name you need or want.