This question is answered by the IRS: https://www.irs.gov/affordable-care-act/employers/questions-and-answers-on-employer-shared-responsibility-provisions-under-the-affordable-care-act
Yes. The employer shared responsibility provisions include a rule that also applies for certain other tax and employee benefit purposes (section 414). Under this rule, two or more businesses that have a certain level of common or related ownership generally are treated as a single employer, and are combined for purposes of determining whether or not they collectively employ at least 50 full-time employees (including full-time equivalent employees). If the combined total meets the ALE threshold, then each separate business is considered to be part of an ALE and is therefore subject to the employer shared responsibility provisions. This includes any business that does not employ enough employees to meet the ALE threshold on its own. Under this rule, an ALE may be a single employer or a group of related employers treated as an aggregated ALE group, which is a group of employers treated as a single employer under section 414(b), (c), (m) or (o). Each employer that is a member of an aggregated ALE group is referred to as an ALE member.
For Example: If an individual owns 80 percent or more of two businesses that are separate legal entities, the total number of full-time employees of that employer is based on the full-time employees (including full-time equivalent employees) in both businesses combined together. If the employees in the combined businesses add up to fewer than 50 full-time employees (including full-time equivalent employees) in a calendar year, the employer shared responsibility provisions will not apply to those businesses for the following calendar year.